Mon Jun 21 18:56:39 UTC 2021 I: starting to build exonerate/bullseye/i386 on jenkins on '2021-06-21 18:56' Mon Jun 21 18:56:39 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/16017/console.log Mon Jun 21 18:56:39 UTC 2021 I: Downloading source for bullseye/exonerate=2.4.0-5 --2021-06-21 18:56:39-- http://cdn-fastly.deb.debian.org/debian/pool/main/e/exonerate/exonerate_2.4.0-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2109 (2.1K) Saving to: ‘exonerate_2.4.0-5.dsc’ 0K .. 100% 14.8M=0s 2021-06-21 18:56:39 (14.8 MB/s) - ‘exonerate_2.4.0-5.dsc’ saved [2109/2109] Mon Jun 21 18:56:39 UTC 2021 I: exonerate_2.4.0-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: exonerate Binary: exonerate Architecture: any Version: 2.4.0-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/exonerate Vcs-Git: https://salsa.debian.org/med-team/exonerate.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libglib2.0-dev, libreadline-dev Package-List: exonerate deb science optional arch=any Checksums-Sha1: 5b119c0aef0fa08c3f4a11014544f2ac5ca8afde 520899 exonerate_2.4.0.orig.tar.gz 69da719216a39755b5ec11dfffda0c32d9ab39f9 9192 exonerate_2.4.0-5.debian.tar.xz Checksums-Sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 520899 exonerate_2.4.0.orig.tar.gz 8008e0266c3af10809bbb8e5de6f9774dcfa413da192bdfa79bad56098762b92 9192 exonerate_2.4.0-5.debian.tar.xz Files: 126fbade003b80b663a1d530c56f1904 520899 exonerate_2.4.0.orig.tar.gz c553b6e4a4b7140f63e052eac3db6be3 9192 exonerate_2.4.0-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/JVhoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF8NQ//URedP/UV7WUNn4jFaiX2Hk2IYgVv9+LE X/ajlGjg9BQoD28Q9FwiRkJCj4GgneI9bBC77ai2zTYOyrcTbDXAim/zlkPa21hF GZioVEj04kgQkd0OVjbjwqF6fpvrmv5C5ntB50uG3bM62SBUQ6Cc2z8nQ802ruN8 HkhCqAJfSiwNuYoRSN0OBKdVkWlswl7/Rzo/Sw7F0fsrsJS6XGxARGKCCvkhMhqc hsu9nHSmrSdNPnLJi7X/ptzs1fliHvrG/WvpykmhckQvJ5YUDEJKgEhkiMvEmmMA 9hDVih0wrVwbW3au+9iTwfZ3tGhSf2On4wUxqD5X3TRJa+OnDNTRq1JjHUATTV8V +AAAXNB6P3G9ky/agmRp4OGMB1sIchjQ4tHntEp6ciZkkWQcV9dxsR/Qo8+E7O4P 42ox50icCJhcB47gN+L7BglktpbvVwptbcd4B0fPffvFEKk6SN1w3JxNzNkXOfJU 5mdb9voQBdhacH/07UascttkitwlBUDW9OjqktpSUWgw4EuEiyZQM+qPyMVSQPMr eT8kEjqtY3YEuqI1X4OaHZjTKIdEZGKfm3U/63eIYwG7yT4CIFSdi8D907rYnKZV EuT/3bbKDWEwVpl5rCGScfYYr38vVYFE6tJFFXxSQk9upjTmaqHR5gV/PiiEziPM Gz8ayBTTCbw= =TFtD -----END PGP SIGNATURE----- Mon Jun 21 18:56:39 UTC 2021 I: Checking whether the package is not for us Mon Jun 21 18:56:39 UTC 2021 I: Starting 1st build on remote node ionos16-i386.debian.net. Mon Jun 21 18:56:39 UTC 2021 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Mon Jun 21 19:06:51 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 24 13:19:39 -12 2022 I: pbuilder-time-stamp: 1658711979 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [exonerate_2.4.0-5.dsc] I: copying [./exonerate_2.4.0.orig.tar.gz] I: copying [./exonerate_2.4.0-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.IEZXAKtG/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 3 09:18:18 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./exonerate_2.4.0-5.dsc dpkg-source: info: extracting exonerate in exonerate-2.4.0 dpkg-source: info: unpacking exonerate_2.4.0.orig.tar.gz dpkg-source: info: unpacking exonerate_2.4.0-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build-as-needed.patch dpkg-source: info: applying manpages.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpagesyntax.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4613/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,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='401cab404b5640e99bc4b12835ea4066' 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='4613' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/pbuilderrc_kV8a --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/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://85.184.249.68:3128' I: uname -a Linux ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 23 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/4613/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libglib2.0-dev, libreadline-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however: Package libglib2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmount-dev{a} libmpdec3{a} libncurses-dev{a} libncurses6{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix2{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline-dev{a} libreadline8{a} libselinux1-dev{a} libsepol1-dev{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} uuid-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 33.4 MB of archives. After unpacking 128 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 uuid-dev i386 2.36.1-7 [99.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libblkid-dev i386 2.36.1-7 [245 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libffi-dev i386 3.3-6 [54.7 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libglib2.0-data all 2.66.8-1 [1164 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libglib2.0-bin i386 2.66.8-1 [144 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libglib2.0-dev-bin i386 2.66.8-1 [179 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libsepol1-dev i386 3.1-1 [377 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libpcre2-16-0 i386 10.36-2 [231 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libpcre2-32-0 i386 10.36-2 [219 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libpcre2-posix2 i386 10.36-2 [49.2 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libpcre2-dev i386 10.36-2 [739 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libselinux1-dev i386 3.1-3 [177 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libmount-dev i386 2.36.1-7 [77.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libpcre16-3 i386 2:8.39-13 [258 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libpcre32-3 i386 2:8.39-13 [249 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libpcrecpp0v5 i386 2:8.39-13 [153 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libpcre3-dev i386 2:8.39-13 [656 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libglib2.0-dev i386 2.66.8-1 [1688 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libncurses-dev i386 6.2+20201114-2 [373 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libreadline-dev i386 8.1-1 [161 kB] Fetched 33.4 MB in 0s (84.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up libffi-dev:i386 (3.3-6) ... Setting up libpcre2-16-0:i386 (10.36-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libpcre2-32-0:i386 (10.36-2) ... Setting up libglib2.0-data (2.66.8-1) ... Setting up uuid-dev:i386 (2.36.1-7) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libpcre32-3:i386 (2:8.39-13) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libpcre2-posix2:i386 (10.36-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libblkid-dev:i386 (2.36.1-7) ... Setting up libncurses-dev:i386 (6.2+20201114-2) ... Setting up gettext (0.21-4) ... Setting up libpcre2-dev:i386 (10.36-2) ... Setting up libtool (2.4.6-15) ... Setting up libselinux1-dev:i386 (3.1-3) ... Setting up libpcre3-dev:i386 (2:8.39-13) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libglib2.0-bin (2.66.8-1) ... Setting up m4 (1.4.18-5) ... Setting up libreadline-dev:i386 (8.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libmount-dev:i386 (2.36.1-7) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up libglib2.0-dev-bin (2.66.8-1) ... Setting up libglib2.0-dev:i386 (2.66.8-1) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: 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 dpkg-buildpackage: info: source package exonerate dpkg-buildpackage: info: source version 2.4.0-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/exonerate-2.4.0' dh_auto_clean rm -rf codegen make[1]: Leaving directory '/build/exonerate-2.4.0' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/exonerate-2.4.0' dh_autoreconf --as-needed aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.in:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.in:9: installing './compile' src/bsdp/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/bsdp/Makefile.am: installing './depcomp' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' parallel-tests: installing './test-driver' src/c4/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/comparison/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/database/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/general/Makefile.am:9: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/hub/Makefile.am:5: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/model/Makefile.am:11: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/program/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/sdp/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/sequence/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/struct/Makefile.am:14: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/util/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') make[1]: Leaving directory '/build/exonerate-2.4.0' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for strings.h... (cached) yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu Set host to i686-pc-linux-gnu i686-pc-linux-gnu *** Unknown build platform: i686-pc-linux-gnu *** Set source_root_dir to /build/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile config.status: executing depfiles commands dh_auto_build make -j18 make[1]: Entering directory '/build/exonerate-2.4.0' Making all in doc make[2]: Entering directory '/build/exonerate-2.4.0/doc' Making all in man make[3]: Entering directory '/build/exonerate-2.4.0/doc/man' Making all in man1 make[4]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/build/exonerate-2.4.0/doc/man' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/exonerate-2.4.0/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/exonerate-2.4.0/doc' Making all in src make[2]: Entering directory '/build/exonerate-2.4.0/src' Making all in struct make[3]: Entering directory '/build/exonerate-2.4.0/src/struct' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fsm.test.o fsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fsm.o fsm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 recyclebin.o recyclebin.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 matrix.test.o matrix.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 matrix.o matrix.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 pqueue.test.o pqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 pqueue.o pqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 slist.test.o slist.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 slist.o slist.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 rangetree.test.o rangetree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 rangetree.o rangetree.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 vfsm.test.o vfsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 vfsm.o vfsm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 recyclebin.test.o recyclebin.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sparsecache.test.o sparsecache.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sparsecache.o sparsecache.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 dejavu.test.o dejavu.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 dejavu.o dejavu.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from rangetree.h:23, from rangetree.c:18: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | 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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bitarray.test.o bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bitarray.o bitarray.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.test.o splaytree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/struct' Making all in general make[3]: Entering directory '/build/exonerate-2.4.0/src/general' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 argument.test.o argument.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 argument.o argument.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 lineparse.test.o lineparse.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 lineparse.o lineparse.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 compoundfile.test.o compoundfile.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 compoundfile.o compoundfile.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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:111, from jobqueue.h:23, from jobqueue.test.c:17: /usr/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here 261 | 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])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 140 | if(!g_strcasecmp(arg_string, false_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c: In function 'Argument_show_version': argument.c:173:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 173 | g_print("Built on %s\n", __DATE__); | ^~~~~~~~ argument.c: In function 'main': argument.c:306:13: warning: Deprecated pre-processor symbol 306 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 307 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:111, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here 261 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 502 | g_tree_traverse(arg->option_registry, Argument_set_env_var_func, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 559 | g_tree_traverse(arg->option_registry, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol, replace with 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol, replace with 169 | g_string_sprintfa(full_msg, "%s", msg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sequence.test.o sequence.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sequence.o sequence.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.o alphabet.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.o translate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.o splice.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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:91, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 317 | if(!g_strcasecmp(name, dna_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 320 | if(!g_strcasecmp(name, protein_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 323 | if(!g_strcasecmp(name, unknown_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 195 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 203 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 make[3]: Entering directory '/build/exonerate-2.4.0/src/comparison' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 wordhood.test.o wordhood.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 wordhood.o wordhood.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hspset.test.o hspset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hspset.o hspset.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.o match.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 273 | if(!g_strcasecmp(force_fsm, "normal")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 275 | if(!g_strcasecmp(force_fsm, "compact")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ 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); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 59 | register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 69 | g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 155 | register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 174 | g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 252 | g_strup(pcr_primer->forward); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 253 | g_strup(pcr_primer->revcomp); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 357 | pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 363 | pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 366 | pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 381 | g_mem_chunk_destroy(pcr->sensor_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 383 | g_mem_chunk_destroy(pcr->probe_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 384 | g_mem_chunk_destroy(pcr->match_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 637 | g_strdown(query_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 638 | g_strdown(target_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 640 | g_strup(query_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 641 | g_strup(target_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/comparison' Making all in database make[3]: Entering directory '/build/exonerate-2.4.0/src/database' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastadb.test.o fastadb.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastadb.o fastadb.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastapipe.test.o fastapipe.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastapipe.o fastapipe.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 dataset.test.o dataset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 dataset.o dataset.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 index.test.o index.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 index.o index.c index.c: In function 'Index_open': index.c:943:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 943 | fread(index->dataset_path, sizeof(gchar), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 944 | index->header->dataset_path_len, index->fp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.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/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/database' Making all in c4 make[3]: Entering directory '/build/exonerate-2.4.0/src/c4' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 region.test.o region.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 region.o region.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 c4.test.o c4.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 c4.o c4.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 alignment.test.o alignment.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 alignment.o alignment.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.test.o codegen.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 667 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 677 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 690 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 988 | g_strup(tg_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/c4' Making all in bsdp make[3]: Entering directory '/build/exonerate-2.4.0/src/bsdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 heuristic.test.o heuristic.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 heuristic.o heuristic.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bsdp.test.o bsdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bsdp.o bsdp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hpair.test.o hpair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hpair.o hpair.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sar.o sar.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sar.test.o sar.test.c gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' Making all in sdp make[3]: Entering directory '/build/exonerate-2.4.0/src/sdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sdp.test.o sdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sdp.o sdp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 boundary.o boundary.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 scheduler.o scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 lookahead.o lookahead.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 straceback.o straceback.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 lookahead.test.o lookahead.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 boundary.test.o boundary.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 scheduler.test.o scheduler.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 straceback.test.o straceback.test.c gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/sdp' Making all in model make[3]: Entering directory '/build/exonerate-2.4.0/src/model' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 edit_distance.test.o edit_distance.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 edit_distance.o edit_distance.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 affine.test.o affine.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 affine.o affine.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 ungapped.o ungapped.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 protein2dna.test.o protein2dna.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 protein2dna.o protein2dna.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 frameshift.o frameshift.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 ner.test.o ner.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 ner.o ner.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 est2genome.test.o est2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 est2genome.o est2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 intron.o intron.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 ungapped.test.o ungapped.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 intron.test.o intron.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 protein2genome.test.o protein2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 protein2genome.o protein2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 phase.o phase.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 coding2coding.test.o coding2coding.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 coding2coding.o coding2coding.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 frameshift.test.o frameshift.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 coding2genome.test.o coding2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 coding2genome.o coding2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 cdna2genome.test.o cdna2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 cdna2genome.o cdna2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 genome2genome.test.o genome2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 genome2genome.o genome2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 phase.test.o phase.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 modeltype.test.o modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 modeltype.o modeltype.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 124 | if(!g_strcasecmp(short_name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 phase.test phase.test.o phase.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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/model' Making all in hub make[3]: Entering directory '/build/exonerate-2.4.0/src/hub' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gam.test.o gam.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gam.o gam.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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.test.o analysis.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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:82, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | 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:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | 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, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | 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, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | 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")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 336 | } else if((!g_strcasecmp(force_scan, "query")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 337 | || (!g_strcasecmp(force_scan, "q"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 339 | } else if((!g_strcasecmp(force_scan, "target")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 340 | || (!g_strcasecmp(force_scan, "t"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/hub' Making all in program make[3]: Entering directory '/build/exonerate-2.4.0/src/program' ../../src/model/bootstrapper --compiled no ** Message: 13:20:08.541: Starting building bootstrapping components ** Message: 13:20:08.541: Processing model [u] ** Message: 13:20:08.541: Bootstrapper processing model [ungapped:dna2dna] ** Message: 13:20:08.541: Process optimal [optimal:ungapped:dna2dna] ** (process:8240): WARNING **: 13:20:08.541: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:8240): WARNING **: 13:20:08.541: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:8240): WARNING **: 13:20:08.541: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] ** (process:8240): WARNING **: 13:20:08.541: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] ** Message: 13:20:08.542: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:08.658: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:08.797: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:08.946: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.147: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.354: 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: 13:20:09.354: 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: 13:20:09.356: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 13:20:09.357: 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: 13:20:09.357: 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: 13:20:09.359: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 13:20:09.359: 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: 13:20:09.359: 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: 13:20:09.361: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 13:20:09.361: 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: 13:20:09.361: 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: 13:20:09.363: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 13:20:09.363: 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: 13:20:09.363: 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: 13:20:09.365: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:20:09.365: Bootstrapper processing model [ungapped:protein2protein] ** Message: 13:20:09.365: Process optimal [optimal:ungapped:protein2protein] ** Message: 13:20:09.366: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.479: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.610: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.749: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:09.945: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:10.162: 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: 13:20:10.162: 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: 13:20:10.244: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 13:20:10.244: 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: 13:20:10.244: 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: 13:20:10.334: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 13:20:10.334: 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: 13:20:10.334: 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: 13:20:10.389: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 13:20:10.389: 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: 13:20:10.389: 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: 13:20:10.429: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 13:20:10.429: 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: 13:20:10.429: 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: 13:20:10.431: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 13:20:10.431: Bootstrapper processing model [ungapped:dna2protein] ** Message: 13:20:10.431: Process optimal [optimal:ungapped:dna2protein] ** Message: 13:20:10.432: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:10.717: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:10.902: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:11.098: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:11.377: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:11.635: 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: 13:20:11.635: 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: 13:20:11.637: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 13:20:11.637: 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: 13:20:11.637: 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: 13:20:11.640: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 13:20:11.640: 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: 13:20:11.640: 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: 13:20:11.643: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 13:20:11.643: 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: 13:20:11.643: 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: 13:20:11.645: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 13:20:11.645: 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: 13:20:11.645: 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: 13:20:11.648: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 13:20:11.648: Bootstrapper processing model [ungapped:protein2dna] ** Message: 13:20:11.648: Process optimal [optimal:ungapped:protein2dna] ** Message: 13:20:11.649: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:11.791: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:11.969: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:12.153: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:12.452: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:12.710: 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: 13:20:12.710: 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: 13:20:12.712: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 13:20:12.712: 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: 13:20:12.712: 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: 13:20:12.715: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 13:20:12.715: 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: 13:20:12.715: 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: 13:20:12.718: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 13:20:12.718: 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: 13:20:12.718: 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: 13:20:12.721: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 13:20:12.721: 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: 13:20:12.721: 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: 13:20:12.724: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 13:20:12.724: Processing model [u:t] ** Message: 13:20:12.724: Bootstrapper processing model [ungapped:codon] ** Message: 13:20:12.724: Process optimal [optimal:ungapped:codon] ** Message: 13:20:12.725: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:12.933: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:13.196: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:13.503: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:13.938: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:14.342: 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: 13:20:14.342: 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: 13:20:14.345: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 13:20:14.345: 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: 13:20:14.345: 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: 13:20:14.348: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 13:20:14.348: 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: 13:20:14.348: 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: 13:20:14.351: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 13:20:14.351: 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: 13:20:14.351: 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: 13:20:14.354: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 13:20:14.354: 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: 13:20:14.354: 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: 13:20:14.358: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 13:20:14.358: Processing model [a:g] ** Message: 13:20:14.359: Bootstrapper processing model [affine:global:dna2dna] ** Message: 13:20:14.359: Process optimal [optimal:affine:global:dna2dna] ** Message: 13:20:14.359: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:14.653: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:15.078: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:15.501: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:16.037: 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: 13:20:16.037: 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: 13:20:16.134: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 13:20:16.134: 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: 13:20:16.134: 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: 13:20:16.141: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 13:20:16.141: 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: 13:20:16.141: 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: 13:20:16.244: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 13:20:16.244: 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: 13:20:16.244: 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: 13:20:16.388: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:20:16.388: Bootstrapper processing model [affine:global:protein2protein] ** Message: 13:20:16.388: Process optimal [optimal:affine:global:protein2protein] ** Message: 13:20:16.389: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:16.788: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:17.380: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:17.850: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:18.439: 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: 13:20:18.439: 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: 13:20:18.475: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 13:20:18.475: 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: 13:20:18.475: 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: 13:20:18.479: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 13:20:18.479: 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: 13:20:18.479: 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: 13:20:18.515: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 13:20:18.515: 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: 13:20:18.515: 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: 13:20:18.519: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 13:20:18.520: Processing model [a:b] ** Message: 13:20:18.520: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 13:20:18.520: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 13:20:18.521: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:18.938: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:19.548: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:20.071: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:20.491: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:20.973: 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: 13:20:20.973: 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: 13:20:20.977: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 13:20:20.977: 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: 13:20:20.977: 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: 13:20:20.981: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 13:20:20.981: 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: 13:20:20.981: 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: 13:20:20.985: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 13:20:20.985: 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: 13:20:20.985: 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: 13:20:20.990: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 13:20:20.990: 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: 13:20:20.990: 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: 13:20:20.993: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:20:20.994: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 13:20:20.994: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 13:20:20.995: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:21.361: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:21.952: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:22.465: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:22.868: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:23.351: 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: 13:20:23.351: 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: 13:20:23.356: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 13:20:23.356: 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: 13:20:23.356: 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: 13:20:23.360: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 13:20:23.360: 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: 13:20:23.360: 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: 13:20:23.364: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 13:20:23.364: 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: 13:20:23.364: 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: 13:20:23.369: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 13:20:23.369: 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: 13:20:23.369: 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: 13:20:23.373: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 13:20:23.373: Processing model [a:l] ** Message: 13:20:23.373: Bootstrapper processing model [affine:local:dna2dna] ** Message: 13:20:23.373: Process optimal [optimal:affine:local:dna2dna] ** Message: 13:20:23.374: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:23.542: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:23.763: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:24.000: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:24.415: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:24.894: 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: 13:20:24.894: 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: 13:20:24.898: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 13:20:24.898: 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: 13:20:24.898: 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: 13:20:24.903: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 13:20:24.903: 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: 13:20:24.903: 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: 13:20:24.907: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 13:20:24.907: 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: 13:20:24.908: 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: 13:20:24.912: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 13:20:24.912: 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: 13:20:24.912: 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: 13:20:24.916: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:20:24.918: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 13:20:24.919: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:25.259: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:25.765: 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: 13:20:25.765: 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: 13:20:25.770: 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: 13:20:25.770: 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: 13:20:25.770: 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: 13:20:25.775: 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: 13:20:25.775: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 13:20:25.776: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:26.087: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:26.527: 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: 13:20:26.527: 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: 13:20:26.532: 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: 13:20:26.532: 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: 13:20:26.532: 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: 13:20:26.537: 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: 13:20:26.537: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 13:20:26.538: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:27.299: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:28.522: 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: 13:20:28.523: 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: 13:20:28.528: 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: 13:20:28.528: 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: 13:20:28.528: 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: 13:20:28.533: 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: 13:20:28.534: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:28.696: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:28.865: 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: 13:20:28.865: 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: 13:20:28.870: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 13:20:28.870: 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: 13:20:28.870: 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: 13:20:28.875: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 13:20:28.876: Bootstrapper processing model [affine:local:protein2protein] ** Message: 13:20:28.876: Process optimal [optimal:affine:local:protein2protein] ** Message: 13:20:28.876: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:29.041: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:29.274: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:29.513: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:29.920: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:30.404: 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: 13:20:30.405: 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: 13:20:30.410: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 13:20:30.410: 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: 13:20:30.410: 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: 13:20:30.416: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 13:20:30.416: 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: 13:20:30.416: 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: 13:20:30.421: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 13:20:30.421: 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: 13:20:30.421: 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: 13:20:30.427: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 13:20:30.427: 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: 13:20:30.427: 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: 13:20:30.433: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 13:20:30.435: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 13:20:30.435: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:30.765: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:31.267: 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: 13:20:31.267: 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: 13:20:31.273: 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: 13:20:31.273: 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: 13:20:31.273: 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: 13:20:31.278: 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: 13:20:31.278: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 13:20:31.279: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:31.562: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:31.977: 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: 13:20:31.977: 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: 13:20:31.982: 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: 13:20:31.982: 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: 13:20:31.982: 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: 13:20:31.988: 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: 13:20:31.988: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 13:20:31.989: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:32.710: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:33.923: 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: 13:20:33.923: 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: 13:20:33.929: 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: 13:20:33.929: 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: 13:20:33.929: 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: 13:20:33.935: 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: 13:20:33.935: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:34.100: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:34.272: 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: 13:20:34.272: 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: 13:20:34.278: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 13:20:34.278: 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: 13:20:34.278: 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: 13:20:34.285: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 13:20:34.285: Processing model [a:o] ** Message: 13:20:34.285: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 13:20:34.285: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 13:20:34.286: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:34.613: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:35.098: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:35.609: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:36.027: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:36.507: 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: 13:20:36.507: 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: 13:20:36.513: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 13:20:36.513: 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: 13:20:36.513: 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: 13:20:36.520: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 13:20:36.520: 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: 13:20:36.520: 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: 13:20:36.526: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 13:20:36.526: 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: 13:20:36.526: 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: 13:20:36.532: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 13:20:36.532: 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: 13:20:36.532: 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: 13:20:36.538: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:20:36.538: Processing model [e2g] ** Message: 13:20:36.539: Bootstrapper processing model [est2genome] ** Message: 13:20:36.539: Process optimal [optimal:est2genome] ** Message: 13:20:36.540: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:37.211: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:38.223: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:39.155: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:41.653: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:45.003: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 13:20:45.003: 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: 13:20:45.010: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 13:20:45.010: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 13:20:45.010: 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: 13:20:45.017: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 13:20:45.017: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 13:20:45.017: 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: 13:20:45.023: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 13:20:45.023: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 13:20:45.023: 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: 13:20:45.030: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 13:20:45.030: 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: 13:20:45.030: 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: 13:20:45.036: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 13:20:45.044: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 13:20:45.045: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:45.981: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:47.534: 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: 13:20:47.534: 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: 13:20:47.541: 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: 13:20:47.541: 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: 13:20:47.541: 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: 13:20:47.548: 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: 13:20:47.548: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 13:20:47.549: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:48.153: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:49.024: 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: 13:20:49.024: 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: 13:20:49.031: 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: 13:20:49.031: 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: 13:20:49.031: 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: 13:20:49.039: 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: 13:20:49.039: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 13:20:49.041: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:50.005: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:51.551: 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: 13:20:51.551: 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: 13:20:51.559: 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: 13:20:51.559: 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: 13:20:51.559: 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: 13:20:51.567: 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: 13:20:51.567: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 13:20:51.568: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:52.151: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:53.016: 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: 13:20:53.017: 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: 13:20:53.024: 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: 13:20:53.024: 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: 13:20:53.024: 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: 13:20:53.032: 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: 13:20:53.032: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 13:20:53.035: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:54.936: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:58.351: 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: 13:20:58.351: 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: 13:20:58.364: 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: 13:20:58.364: 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: 13:20:58.364: 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: 13:20:58.372: 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: 13:20:58.372: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 13:20:58.373: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:58.984: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:20:59.888: 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: 13:20:59.888: 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: 13:20:59.896: 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: 13:20:59.896: 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: 13:20:59.896: 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_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: 13:20:59.905: 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: 13:20:59.905: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 13:20:59.907: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:02.732: 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: 13:21:02.732: 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: 13:21:02.741: 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: 13:21:02.741: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 13:21:02.743: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:03.801: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:05.546: 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: 13:21:05.546: 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: 13:21:05.555: 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: 13:21:05.555: 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: 13:21:05.555: 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: 13:21:05.564: 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: 13:21:05.564: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 13:21:05.567: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:07.480: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:10.884: 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: 13:21:10.884: 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: 13:21:10.893: 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: 13:21:10.893: 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: 13:21:10.893: 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: 13:21:10.902: 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: 13:21:10.902: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 13:21:10.904: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:11.519: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:12.401: 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: 13:21:12.401: 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: 13:21:12.410: 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: 13:21:12.410: 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: 13:21:12.411: 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: 13:21:12.420: 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: 13:21:12.420: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 13:21:12.423: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:15.195: 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: 13:21:15.195: 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: 13:21:15.209: 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: 13:21:15.209: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 13:21:15.211: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:16.256: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:17.966: 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: 13:21:17.966: 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: 13:21:17.983: 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: 13:21:17.983: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 13:21:17.983: 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_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: 13:21:17.998: 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: 13:21:17.999: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:18.304: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:18.643: 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: 13:21:18.643: 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: 13:21:18.653: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 13:21:18.653: 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: 13:21:18.653: 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: 13:21:18.663: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 13:21:18.664: Processing model [ner] ** Message: 13:21:18.664: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 13:21:18.664: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 13:21:18.664: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:18.866: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:19.134: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:19.417: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:19.956: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:20.622: 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: 13:21:20.622: 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: 13:21:20.632: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 13:21:20.632: 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: 13:21:20.632: 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: 13:21:20.643: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 13:21:20.643: 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: 13:21:20.643: 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: 13:21:20.653: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 13:21:20.653: 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: 13:21:20.653: 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: 13:21:20.664: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 13:21:20.664: 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: 13:21:20.664: 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: 13:21:20.674: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 13:21:20.678: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 13:21:20.679: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:21.140: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:21.852: 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: 13:21:21.852: 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: 13:21:21.862: 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: 13:21:21.862: 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_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 13:21:21.862: 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_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: 13:21:21.873: 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: 13:21:21.873: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 13:21:21.874: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:22.243: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:22.779: 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: 13:21:22.779: 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: 13:21:22.789: 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: 13:21:22.789: 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: 13:21:22.789: 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: 13:21:22.800: 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: 13:21:22.800: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 13:21:22.802: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:23.872: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:25.770: 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: 13:21:25.770: 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: 13:21:25.782: 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: 13:21:25.782: 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: 13:21:25.782: 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: 13:21:25.792: 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: 13:21:25.793: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 13:21:25.794: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:26.184: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:26.762: 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: 13:21:26.762: 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: 13:21:26.774: 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: 13:21:26.774: 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: 13:21:26.774: 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: 13:21:26.785: 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: 13:21:26.785: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 13:21:26.788: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:28.467: 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: 13:21:28.467: 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: 13:21:28.478: 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: 13:21:28.478: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 13:21:28.479: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:28.998: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:29.848: 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: 13:21:29.848: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_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: 13:21:29.859: 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: 13:21:29.860: 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: 13:21:29.860: 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: 13:21:29.871: 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: 13:21:29.872: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:30.057: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:30.257: 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: 13:21:30.257: 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: 13:21:30.269: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 13:21:30.269: 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: 13:21:30.269: 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: 13:21:30.280: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 13:21:30.281: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 13:21:30.281: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 13:21:30.281: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:30.483: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:30.749: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:31.022: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:31.565: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:32.235: 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: 13:21:32.235: 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: 13:21:32.248: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 13:21:32.248: 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: 13:21:32.248: 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: 13:21:32.259: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 13:21:32.259: 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: 13:21:32.259: 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: 13:21:32.271: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 13:21:32.271: 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: 13:21:32.271: 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: 13:21:32.282: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 13:21:32.283: 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: 13:21:32.283: 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: 13:21:32.294: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 13:21:32.298: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 13:21:32.299: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:32.741: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:33.449: 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: 13:21:33.449: 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: 13:21:33.461: 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: 13:21:33.461: 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: 13:21:33.461: 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: 13:21:33.473: 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: 13:21:33.473: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 13:21:33.474: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:33.830: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:34.378: 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: 13:21:34.378: 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: 13:21:34.390: 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: 13:21:34.390: 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: 13:21:34.390: 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: 13:21:34.403: 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: 13:21:34.403: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 13:21:34.405: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:35.452: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:37.318: 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: 13:21:37.318: 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: 13:21:37.334: 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: 13:21:37.334: 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: 13:21:37.334: 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: 13:21:37.348: 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: 13:21:37.348: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 13:21:37.349: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:37.759: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:38.346: 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: 13:21:38.346: 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: 13:21:38.359: 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: 13:21:38.359: 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: 13:21:38.359: 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: 13:21:38.372: 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: 13:21:38.372: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 13:21:38.375: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:40.068: 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: 13:21:40.068: 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: 13:21:40.086: 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: 13:21:40.086: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 13:21:40.087: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:40.585: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:41.423: 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: 13:21:41.424: 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: 13:21:41.436: 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: 13:21:41.436: 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: 13:21:41.436: 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: 13:21:41.449: 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: 13:21:41.450: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:41.634: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:41.840: 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: 13:21:41.841: 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: 13:21:41.854: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 13:21:41.854: 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: 13:21:41.855: 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: 13:21:41.869: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 13:21:41.869: Processing model [p2d] ** Message: 13:21:41.869: Bootstrapper processing model [protein2dna:local] ** Message: 13:21:41.869: Process optimal [optimal:protein2dna:local] ** Message: 13:21:41.870: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:42.193: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:42.681: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:43.179: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:44.317: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:45.616: 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: 13:21:45.616: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_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: 13:21:45.631: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 13:21:45.631: 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: 13:21:45.631: 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: 13:21:45.646: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 13:21:45.646: 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: 13:21:45.646: 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: 13:21:45.661: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 13:21:45.661: 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: 13:21:45.661: 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: 13:21:45.676: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 13:21:45.676: 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: 13:21:45.676: 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: 13:21:45.690: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 13:21:45.697: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 13:21:45.699: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:46.548: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:48.042: 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: 13:21:48.042: 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: 13:21:48.056: 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: 13:21:48.056: 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: 13:21:48.056: 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: 13:21:48.070: 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: 13:21:48.070: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 13:21:48.071: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:48.589: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:49.597: 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: 13:21:49.597: 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: 13:21:49.612: 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: 13:21:49.612: 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: 13:21:49.612: 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: 13:21:49.650: 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: 13:21:49.650: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 13:21:49.652: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:51.304: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:54.345: 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: 13:21:54.345: 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: 13:21:54.361: 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: 13:21:54.361: 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: 13:21:54.361: 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: 13:21:54.380: 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: 13:21:54.380: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:54.589: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:54.797: 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: 13:21:54.797: 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: 13:21:54.812: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 13:21:54.812: 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: 13:21:54.812: 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: 13:21:54.828: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 13:21:54.828: Processing model [p2d:b] ** Message: 13:21:54.829: Bootstrapper processing model [protein2dna:bestfit] ** Message: 13:21:54.829: Process optimal [optimal:protein2dna:bestfit] ** Message: 13:21:54.831: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:55.845: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:57.649: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:21:59.156: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:00.320: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:01.661: 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: 13:22:01.661: 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: 13:22:01.676: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 13:22:01.676: 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: 13:22:01.676: 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: 13:22:01.694: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 13:22:01.695: 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: 13:22:01.695: 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: 13:22:01.708: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 13:22:01.708: 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: 13:22:01.708: 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: 13:22:01.724: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 13:22:01.724: 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: 13:22:01.724: 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: 13:22:01.755: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 13:22:01.755: Processing model [p2g] ** Message: 13:22:01.756: Bootstrapper processing model [protein2genome:local] ** Message: 13:22:01.756: Process optimal [optimal:protein2genome:local] ** Message: 13:22:01.757: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:02.694: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:04.193: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:05.444: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:09.693: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:15.466: 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: 13:22:15.466: 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: 13:22:15.491: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 13:22:15.491: 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: 13:22:15.491: 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: 13:22:15.507: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 13:22:15.507: 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: 13:22:15.507: 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: 13:22:15.530: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 13:22:15.530: 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: 13:22:15.530: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_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: 13:22:15.569: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 13:22:15.569: 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: 13:22:15.569: 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: 13:22:15.596: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 13:22:15.625: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 13:22:15.629: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:19.187: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:26.253: 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: 13:22:26.253: 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: 13:22:26.275: 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: 13:22:26.276: 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: 13:22:26.276: 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: 13:22:26.299: 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: 13:22:26.299: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 13:22:26.302: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:28.173: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:31.322: 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: 13:22:31.322: 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: 13:22:31.344: 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: 13:22:31.344: 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: 13:22:31.344: 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: 13:22:31.368: 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: 13:22:31.368: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 13:22:31.375: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:40.047: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:57.791: 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: 13:22:57.792: 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: 13:22:57.809: 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: 13:22:57.809: 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: 13:22:57.809: 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: 13:22:57.827: 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: 13:22:57.827: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 13:22:57.829: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:22:59.773: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:03.244: 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: 13:23:03.244: 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: 13:23:03.268: 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: 13:23:03.268: 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: 13:23:03.268: 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: 13:23:03.294: 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: 13:23:03.294: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 13:23:03.301: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:18.084: 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: 13:23:18.084: 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: 13:23:18.108: 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: 13:23:18.108: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 13:23:18.113: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:21.923: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:30.286: 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: 13:23:30.286: 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: 13:23:30.315: 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: 13:23:30.315: 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: 13:23:30.315: 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: 13:23:30.340: 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: 13:23:30.341: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 13:23:30.343: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:32.543: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:36.223: 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: 13:23:36.223: 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: 13:23:36.243: 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: 13:23:36.243: 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: 13:23:36.243: 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: 13:23:36.265: 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: 13:23:36.265: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 13:23:36.272: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:50.665: 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: 13:23:50.665: 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: 13:23:50.691: 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: 13:23:50.691: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 13:23:50.695: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:23:54.605: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:02.270: 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: 13:24:02.270: 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: 13:24:02.295: 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: 13:24:02.295: 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: 13:24:02.295: 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: 13:24:02.322: 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: 13:24:02.322: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 13:24:02.325: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:04.279: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:07.509: 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: 13:24:07.509: 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: 13:24:07.538: 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: 13:24:07.538: 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: 13:24:07.538: 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: 13:24:07.561: 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: 13:24:07.561: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 13:24:07.568: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:21.603: 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: 13:24:21.603: 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: 13:24:21.631: 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: 13:24:21.631: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 13:24:21.635: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:25.485: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:33.093: 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: 13:24:33.093: 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: 13:24:33.121: 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: 13:24:33.121: 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: 13:24:33.121: 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: 13:24:33.146: 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: 13:24:33.148: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:33.456: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:33.816: 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: 13:24:33.816: 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: 13:24:33.838: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 13:24:33.838: 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: 13:24:33.838: 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: 13:24:33.860: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 13:24:33.860: Processing model [p2g:b] ** Message: 13:24:33.861: Bootstrapper processing model [protein2genome:bestfit] ** Message: 13:24:33.861: Process optimal [optimal:protein2genome:bestfit] ** Message: 13:24:33.866: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:38.482: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:47.503: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:53.259: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:24:57.497: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:03.322: 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: 13:25:03.322: 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: 13:25:03.357: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 13:25:03.357: 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: 13:25:03.357: 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: 13:25:03.384: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 13:25:03.385: 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: 13:25:03.385: 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: 13:25:03.426: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 13:25:03.426: 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: 13:25:03.426: 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: 13:25:03.458: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 13:25:03.458: 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: 13:25:03.458: 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: 13:25:03.562: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 13:25:03.562: Processing model [c2c] ** Message: 13:25:03.563: Bootstrapper processing model [coding2coding] ** Message: 13:25:03.563: Process optimal [optimal:coding2coding] ** Message: 13:25:03.564: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:04.296: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:05.589: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:06.863: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:10.047: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:14.290: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 13:25:14.290: 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: 13:25:14.321: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 13:25:14.321: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 13:25:14.321: 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: 13:25:14.350: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 13:25:14.350: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 13:25:14.350: 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: 13:25:14.418: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 13:25:14.418: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 13:25:14.418: 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: 13:25:14.448: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 13:25:14.448: 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: 13:25:14.448: 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: 13:25:14.529: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 13:25:14.556: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 13:25:14.560: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:17.153: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:22.734: 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: 13:25:22.734: 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: 13:25:22.761: 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: 13:25:22.761: 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: 13:25:22.761: 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: 13:25:22.788: 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: 13:25:22.788: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 13:25:22.791: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:24.119: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:26.409: 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: 13:25:26.409: 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: 13:25:26.436: 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: 13:25:26.436: 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: 13:25:26.436: 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: 13:25:26.463: 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: 13:25:26.463: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 13:25:26.469: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:32.159: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:43.606: 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: 13:25:43.606: 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: 13:25:43.632: 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: 13:25:43.632: 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: 13:25:43.632: 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: 13:25:43.661: 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: 13:25:43.662: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:43.931: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:44.247: 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: 13:25:44.247: 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: 13:25:44.423: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 13:25:44.423: 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: 13:25:44.423: 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: 13:25:44.502: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 13:25:44.503: Processing model [c2g] ** Message: 13:25:44.504: Bootstrapper processing model [coding2genome] ** Message: 13:25:44.504: Process optimal [optimal:coding2genome] ** Message: 13:25:44.506: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:47.207: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:52.368: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:25:56.348: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:26:11.673: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:26:35.886: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 13:26:35.886: 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: 13:26:35.924: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 13:26:35.924: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 13:26:35.924: 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: 13:26:35.951: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 13:26:35.951: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 13:26:35.951: 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: 13:26:36.034: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 13:26:36.034: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 13:26:36.034: 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: 13:26:36.076: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 13:26:36.076: 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: 13:26:36.076: 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: 13:26:36.239: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 13:26:36.240: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:26:36.610: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:26:37.020: 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: 13:26:37.020: 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: 13:26:37.048: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 13:26:37.048: 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: 13:26:37.049: 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: 13:26:37.078: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 13:26:37.078: Processing model [cd2g] ** Message: 13:26:37.079: Bootstrapper processing model [cdna2genome] ** Message: 13:26:37.079: Process optimal [optimal:cdna2genome] ** Message: 13:26:37.085: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:26:45.121: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:27:00.381: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:27:12.157: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:28:05.454: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:29:34.526: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 13:29:34.526: 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: 13:29:34.596: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 13:29:34.596: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 13:29:34.596: 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: 13:29:34.634: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 13:29:34.634: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 13:29:34.634: 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: 13:29:34.678: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 13:29:34.678: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 13:29:34.678: 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: 13:29:34.830: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 13:29:34.830: 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: 13:29:34.830: 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: 13:29:34.864: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 13:29:34.865: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:29:35.545: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:29:36.431: 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: 13:29:36.431: 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: 13:29:36.648: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 13:29:36.648: 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: 13:29:36.648: 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: 13:29:36.995: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 13:29:36.995: Compiling with: [gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 13:29:37.270: Adding: [c4_model_lookup.o] ** Message: 13:29:37.270: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 13:29:37.481: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 13:29:37.716: Done ** Message: 13:29:37.717: 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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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../../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\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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../../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\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/sdp/scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 265 | g_strup(primer_b); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | 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 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol, replace with 354 | g_string_sprintfa(str, " %d %d %d", | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol, replace with 357 | g_string_sprintfa(str, "\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 make[4]: Leaving directory '/build/exonerate-2.4.0/src/program' make[3]: Leaving directory '/build/exonerate-2.4.0/src/program' Making all in util make[3]: Entering directory '/build/exonerate-2.4.0/src/util' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastaclean.o fastaclean.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastaclip.o fastaclip.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastachecksum.o fastachecksum.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastacomposition.o fastacomposition.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastadiff.o fastadiff.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ 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:82, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ 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)); | ^~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/include/glib-2.0/glib/gfileutils.h:205:14: note: declared here 205 | const gchar *g_basename (const gchar *file_name); | ^~~~~~~~~~ fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 132 | else if(!g_strcasecmp(sort_key, "len")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 134 | else if(!g_strcasecmp(sort_key, "seq")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | 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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong 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directory '/build/exonerate-2.4.0/test/data' Making all in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making all in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making all in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making all in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making all in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Entering directory '/build/exonerate-2.4.0' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/exonerate-2.4.0' make[1]: Leaving directory '/build/exonerate-2.4.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/exonerate-2.4.0' /usr/bin/make -C test check make[2]: Entering directory '/build/exonerate-2.4.0/test' Making check in data make[3]: Entering directory '/build/exonerate-2.4.0/test/data' Making check in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making check in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making check in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[5]: Entering directory '/build/exonerate-2.4.0/test/exonerate' PASS: exonerate.simple.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making check in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[5]: Entering directory '/build/exonerate-2.4.0/test/ipcress' PASS: ipcress.simple.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making check in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/util' make[5]: Entering directory '/build/exonerate-2.4.0/test/util' PASS: fastaclean.test.sh PASS: fastaclip.test.sh PASS: fastacomposition.test.sh PASS: fastadiff.test.sh PASS: fastaexpode.test.sh PASS: fastaindex.fastafetch.test.sh PASS: fastalength.test.sh PASS: fastanrdb.test.sh PASS: fastaoverlap.test.sh PASS: fastarefomat.test.sh PASS: fastaremove.test.sh PASS: fastarevcomp.test.sh PASS: fastasoftmask.fastahardmask.test.sh PASS: fastasort.test.sh PASS: fastasplit.test.sh PASS: fastasubseq.test.sh PASS: fastatranslate.test.sh PASS: fastavalidcds.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 18 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/util' make[4]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[1]: Leaving directory '/build/exonerate-2.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j18 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' Making install in man make[3]: Entering directory '/build/exonerate-2.4.0/doc/man' Making install in man1 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/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' make[4]: Entering directory '/build/exonerate-2.4.0/doc/man' make[5]: Entering directory '/build/exonerate-2.4.0/doc/man' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/exonerate-2.4.0/doc' make[4]: Entering directory '/build/exonerate-2.4.0/doc' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc' make[3]: Leaving directory '/build/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/exonerate-2.4.0/doc' Making install in src make[2]: Entering directory '/build/exonerate-2.4.0/src' Making install in struct make[3]: Entering directory '/build/exonerate-2.4.0/src/struct' make[4]: Entering directory '/build/exonerate-2.4.0/src/struct' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/struct' make[3]: Leaving directory '/build/exonerate-2.4.0/src/struct' Making install in general make[3]: Entering directory '/build/exonerate-2.4.0/src/general' make[4]: Entering directory '/build/exonerate-2.4.0/src/general' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/general' make[3]: Leaving directory '/build/exonerate-2.4.0/src/general' Making install in sequence make[3]: Entering directory '/build/exonerate-2.4.0/src/sequence' make[4]: Entering directory '/build/exonerate-2.4.0/src/sequence' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/sequence' make[3]: Leaving directory '/build/exonerate-2.4.0/src/sequence' Making install in comparison make[3]: Entering directory '/build/exonerate-2.4.0/src/comparison' make[4]: Entering directory '/build/exonerate-2.4.0/src/comparison' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/comparison' make[3]: Leaving directory '/build/exonerate-2.4.0/src/comparison' Making install in database make[3]: Entering directory '/build/exonerate-2.4.0/src/database' make[4]: Entering directory '/build/exonerate-2.4.0/src/database' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/database' make[3]: Leaving directory '/build/exonerate-2.4.0/src/database' Making install in c4 make[3]: Entering directory '/build/exonerate-2.4.0/src/c4' make[4]: Entering directory '/build/exonerate-2.4.0/src/c4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/c4' make[3]: Leaving directory '/build/exonerate-2.4.0/src/c4' Making install in bsdp make[3]: Entering directory '/build/exonerate-2.4.0/src/bsdp' make[4]: Entering directory '/build/exonerate-2.4.0/src/bsdp' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' make[3]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' Making install in sdp make[3]: Entering directory '/build/exonerate-2.4.0/src/sdp' make[4]: Entering directory '/build/exonerate-2.4.0/src/sdp' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/sdp' make[3]: Leaving directory '/build/exonerate-2.4.0/src/sdp' Making install in model make[3]: Entering directory '/build/exonerate-2.4.0/src/model' make[4]: Entering directory '/build/exonerate-2.4.0/src/model' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/model' make[3]: Leaving directory '/build/exonerate-2.4.0/src/model' Making install in hub make[3]: Entering directory '/build/exonerate-2.4.0/src/hub' make[4]: Entering directory '/build/exonerate-2.4.0/src/hub' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/hub' make[3]: Leaving directory '/build/exonerate-2.4.0/src/hub' Making install in program make[3]: Entering directory '/build/exonerate-2.4.0/src/program' make install-am 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/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' make[3]: Leaving directory '/build/exonerate-2.4.0/src/program' 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' make[4]: Nothing to be done for 'install-data-am'. /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' make[3]: Entering directory '/build/exonerate-2.4.0/src' make[4]: Entering directory '/build/exonerate-2.4.0/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src' make[3]: Leaving directory '/build/exonerate-2.4.0/src' make[2]: Leaving directory '/build/exonerate-2.4.0/src' Making install in test make[2]: Entering directory '/build/exonerate-2.4.0/test' Making install in data make[3]: Entering directory '/build/exonerate-2.4.0/test/data' Making install in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[5]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making install in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[5]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[5]: Entering directory '/build/exonerate-2.4.0/test/data' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making install in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making install in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making install in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' make[4]: Entering directory '/build/exonerate-2.4.0/test/util' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[4]: Entering directory '/build/exonerate-2.4.0/test' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test' make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Entering directory '/build/exonerate-2.4.0' make[3]: Entering directory '/build/exonerate-2.4.0' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/exonerate-2.4.0' make[2]: Leaving directory '/build/exonerate-2.4.0' make[1]: Leaving directory '/build/exonerate-2.4.0' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/exonerate-2.4.0' dh_installchangelogs -k ChangeLog make[1]: Leaving directory '/build/exonerate-2.4.0' debian/rules override_dh_installexamples make[1]: Entering directory '/build/exonerate-2.4.0' dh_installexamples mkdir -p /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples; cp -a test/* /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples/; find /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples \( -name "Makefile*" -o -name "*.log" -o -name "*.trs" \) -exec rm \{\} \; for testfile in `find /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples -name "*.sh"` ; do \ sed -i -e "s#../../src/util/#/usr/bin/#" \ -e "s#../../src/program/#/usr/bin/#" \ -e "s#../data/#./data/#" \ ${testfile} ; \ done make[1]: Leaving directory '/build/exonerate-2.4.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'exonerate-dbgsym' in '../exonerate-dbgsym_2.4.0-5_i386.deb'. dpkg-deb: building package 'exonerate' in '../exonerate_2.4.0-5_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../exonerate_2.4.0-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4613 and its subdirectories I: Current time: Sun Jul 24 13:29:49 -12 2022 I: pbuilder-time-stamp: 1658712589 Mon Jun 21 19:06:52 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Mon Jun 21 19:06:52 UTC 2021 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Mon Jun 21 19:37:22 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. Mon Jun 21 19:37:22 UTC 2021 I: exonerate_2.4.0-5_i386.changes: Format: 1.8 Date: Thu, 03 Dec 2020 21:56:27 +0100 Source: exonerate Binary: exonerate exonerate-dbgsym Architecture: i386 Version: 2.4.0-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: exonerate - generic tool for pairwise sequence comparison Changes: exonerate (2.4.0-5) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Update watch file format version to 4. * Set field Upstream-Name in debian/copyright. * Refer to specific version of license GPL-3+. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: 0cf40f93a381a9c4670a4bfdfce682a4827d543a 5367688 exonerate-dbgsym_2.4.0-5_i386.deb bc2eea0af57493ab6bd49f13360ce75def90bf64 6067 exonerate_2.4.0-5_i386.buildinfo cd58b1e0f1b8773c6e3fb88262ce0055c1b49591 1749728 exonerate_2.4.0-5_i386.deb Checksums-Sha256: 21044e77013111e086a6df4843f53652915963c7f76814cc896feaba8cad375b 5367688 exonerate-dbgsym_2.4.0-5_i386.deb 666d5afbaa01f72c52ef5533ef0e4097c079158bbc0399e7ab98ea5785019c2d 6067 exonerate_2.4.0-5_i386.buildinfo a04c3898caa9d8db937c4cfb1c47247280d9281727a6cb9498cdd6a8f9fa73ac 1749728 exonerate_2.4.0-5_i386.deb Files: 2325c6ff5b16595b9ed7919a4a987dc1 5367688 debug optional exonerate-dbgsym_2.4.0-5_i386.deb 276987408e9febc8e20ddfbcf1672135 6067 science optional exonerate_2.4.0-5_i386.buildinfo a14739ee7655b83393ba3168daaee396 1749728 science optional exonerate_2.4.0-5_i386.deb Mon Jun 21 19:37:25 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/exonerate_2.4.0-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/exonerate_2.4.0-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/exonerate_2.4.0-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/b1/exonerate_2.4.0-5_i386.changes /srv/reproducible-results/rbuild-debian/tmp.degaNOE1kG/b2/exonerate_2.4.0-5_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.933s) 0.933s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.180s) 0.180s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jun 21 19:37:28 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Mon Jun 21 19:37:28 UTC 2021 I: exonerate from bullseye built successfully and reproducibly on i386. Mon Jun 21 19:37:30 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jun 21 19:37:30 UTC 2021 I: Submitting 8.0K b1/exonerate_2.4.0-5_i386.buildinfo.asc Mon Jun 21 19:37:31 UTC 2021 I: Submitting 8.0K b2/exonerate_2.4.0-5_i386.buildinfo.asc Mon Jun 21 19:37:31 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jun 21 19:37:31 UTC 2021 I: Done submitting .buildinfo files. Mon Jun 21 19:37:31 UTC 2021 I: Removing signed exonerate_2.4.0-5_i386.buildinfo.asc files: removed './b1/exonerate_2.4.0-5_i386.buildinfo.asc' removed './b2/exonerate_2.4.0-5_i386.buildinfo.asc'