I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 3 16:56:24 -12 2023 I: pbuilder-time-stamp: 1672808184 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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: Copying source file I: copying [exonerate_2.4.0-4.dsc] I: copying [./exonerate_2.4.0.orig.tar.gz] I: copying [./exonerate_2.4.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Jan 6 09:20:11 2019 -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_2.4.0-4.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_2.4.0-4.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2674292/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='157130b6987d4a3ba8bfa3e8edb5ba95' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2674292' 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.aLEfjrJhtz/pbuilderrc_7MNh --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.aLEfjrJhtz/b1 --logfile b1/build.log exonerate_2.4.0-4.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/2674292/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), 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 ... 19195 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{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} libicu63{a} libmagic-mgc{a} libmagic1{a} libmount-dev{a} libmpdec2{a} libncurses-dev{a} libncurses6{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline-dev{a} libreadline7{a} libselinux1-dev{a} libsepol1-dev{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} pkg-config{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} uuid-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 131 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 uuid-dev amd64 2.33.1-0.1 [93.6 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libblkid-dev amd64 2.33.1-0.1 [225 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libffi-dev amd64 3.2.1-9 [156 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libglib2.0-data all 2.58.3-2+deb10u3 [1111 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libglib2.0-bin amd64 2.58.3-2+deb10u3 [126 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libglib2.0-dev-bin amd64 2.58.3-2+deb10u3 [158 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libmount-dev amd64 2.33.1-0.1 [232 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libpcre16-3 amd64 2:8.39-12 [259 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libpcre32-3 amd64 2:8.39-12 [250 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libpcrecpp0v5 amd64 2:8.39-12 [152 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libpcre3-dev amd64 2:8.39-12 [650 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libsepol1-dev amd64 2.8-1 [338 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libselinux1-dev amd64 2.8-1+b1 [169 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libglib2.0-dev amd64 2.58.3-2+deb10u3 [1484 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libreadline-dev amd64 7.0-5 [133 kB] Fetched 31.9 MB in 0s (64.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../2-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../3-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../4-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../5-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../6-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../7-libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../8-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../9-python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... Selecting previously unselected package python3-minimal. (Reading database ... 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No schema files found: doing nothing. Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libsepol1-dev:amd64 (2.8-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libffi-dev:amd64 (3.2.1-9) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libglib2.0-data (2.58.3-2+deb10u3) ... Setting up uuid-dev:amd64 (2.33.1-0.1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libpcre32-3:amd64 (2:8.39-12) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libblkid-dev:amd64 (2.33.1-0.1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up libpcre3-dev:amd64 (2:8.39-12) ... Setting up libglib2.0-bin (2.58.3-2+deb10u3) ... Setting up m4 (1.4.18-2) ... Setting up libreadline-dev:amd64 (7.0-5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libmount-dev:amd64 (2.33.1-0.1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up gettext (0.19.8.1-9) ... Setting up libselinux1-dev:amd64 (2.8-1+b1) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up libglib2.0-dev-bin (2.58.3-2+deb10u3) ... Setting up po-debconf (1.0.21) ... Setting up libglib2.0-dev:amd64 (2.58.3-2+deb10u3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/exonerate-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../exonerate_2.4.0-4_source.changes dpkg-buildpackage: info: source package exonerate dpkg-buildpackage: info: source version 2.4.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build dh build 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu Set host to x86_64-pc-linux-gnu x86_64-pc-linux-gnu Customising build for X86_64 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 configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j16 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sparsecache.o sparsecache.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o dejavu.o dejavu.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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.test.o bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.o bitarray.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.test.o splaytree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.o splaytree.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.test.o noitree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.o noitree.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] fread(&num, sizeof(guint64), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o matrix.test matrix.test.o matrix.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[3]: Leaving directory '/build/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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.o jobqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.test.o threadref.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.o threadref.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 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] g_print("Built on %s\n", __DATE__); ^~~~~~~~ argument.c: In function 'main': argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 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:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ jobqueue.test.c: In function 'main': jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 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:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lineparse.test lineparse.test.o lineparse.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o argument.test argument.test.o argument.o -lglib-2.0 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.test.o alphabet.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.test.o codonsubmat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.o codonsubmat.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 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] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 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] 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 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] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o submat.test submat.test.o submat.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[3]: Leaving directory '/build/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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.o seeder.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 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 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] 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 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] 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 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] 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 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] 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 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] 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 gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 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] 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 void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 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 void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 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 void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o index.o index.c dataset.c: In function 'Dataset_info': dataset.c:305:13: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] g_print("Sequence Dataset:\n" ^~~~~~~~~~~~~~~~~~~~~ dataset.c:316:13: dataset->header->number_of_seqs, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataset.c:310:39: note: format string is defined here " number of sequences: %lld\n" ~~~^ %ld dataset.c:305:13: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] g_print("Sequence Dataset:\n" ^~~~~~~~~~~~~~~~~~~~~ dataset.c:317:13: dataset->header->max_seq_len); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataset.c:311:39: note: format string is defined here " longest sequence: %lld\n\n", ~~~^ %ld index.c: In function 'Index_open': index.c:943:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index->dataset_path, sizeof(gchar), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ index->header->dataset_path_len, index->fp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.test.o viterbi.test.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.o opair.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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.test.o subopt.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.test.o cgutil.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o region.test region.test.o region.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sar.test.o sar.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.test.o boundary.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.test.o scheduler.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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/x86_64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.test.o straceback.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.test.o modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.o modeltype.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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/x86_64-linux-gnu/glib-2.0/include\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bootstrapper.o bootstrapper.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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] 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 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] 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 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] 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 void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 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] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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: 16:57:15.424: Starting building bootstrapping components ** Message: 16:57:15.424: Processing model [u] ** Message: 16:57:15.425: Bootstrapper processing model [ungapped:dna2dna] ** Message: 16:57:15.425: Process optimal [optimal:ungapped:dna2dna] ** (process:2720229): WARNING **: 16:57:15.425: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:2720229): WARNING **: 16:57:15.425: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:2720229): WARNING **: 16:57:15.425: Creating codegen directory [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] ** (process:2720229): WARNING **: 16:57:15.425: Creating codegen directory [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] ** Message: 16:57:15.425: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 16:57:15.697: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 16:57:15.961: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 16:57:16.224: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:57:16.563: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:57:16.933: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 16:57:16.933: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 16:57:16.939: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 16:57:16.939: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 16:57:16.939: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 16:57:16.944: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 16:57:16.944: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 16:57:16.944: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 16:57:16.949: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 16:57:16.949: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:57:16.949: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:57:16.954: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 16:57:16.955: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:57:16.955: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:57:16.959: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:57:16.959: Bootstrapper processing model [ungapped:protein2protein] ** Message: 16:57:16.959: Process optimal [optimal:ungapped:protein2protein] ** Message: 16:57:16.959: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 16:57:17.178: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 16:57:17.423: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 16:57:17.737: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:57:18.098: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:57:18.549: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 16:57:18.549: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 16:57:18.553: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 16:57:18.554: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 16:57:18.554: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 16:57:18.558: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 16:57:18.558: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 16:57:18.558: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 16:57:18.562: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 16:57:18.563: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:57:18.563: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:57:18.567: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 16:57:18.567: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:57:18.567: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:57:18.572: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:57:18.572: Bootstrapper processing model [ungapped:dna2protein] ** Message: 16:57:18.572: Process optimal [optimal:ungapped:dna2protein] ** Message: 16:57:18.573: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 16:57:18.905: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 16:57:19.418: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 16:57:19.906: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 16:57:20.478: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 16:57:21.028: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 16:57:21.028: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 16:57:21.033: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 16:57:21.033: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 16:57:21.033: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 16:57:21.038: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 16:57:21.038: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 16:57:21.038: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 16:57:21.054: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 16:57:21.054: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 16:57:21.054: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 16:57:21.081: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 16:57:21.081: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 16:57:21.081: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 16:57:21.098: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 16:57:21.098: Bootstrapper processing model [ungapped:protein2dna] ** Message: 16:57:21.098: Process optimal [optimal:ungapped:protein2dna] ** Message: 16:57:21.098: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 16:57:21.445: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 16:57:21.877: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 16:57:22.365: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 16:57:22.930: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 16:57:23.417: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 16:57:23.417: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 16:57:23.425: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 16:57:23.425: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 16:57:23.425: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 16:57:23.431: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 16:57:23.431: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 16:57:23.431: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 16:57:23.438: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 16:57:23.438: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 16:57:23.438: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 16:57:23.443: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 16:57:23.443: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 16:57:23.443: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 16:57:23.449: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 16:57:23.449: Processing model [u:t] ** Message: 16:57:23.450: Bootstrapper processing model [ungapped:codon] ** Message: 16:57:23.450: Process optimal [optimal:ungapped:codon] ** Message: 16:57:23.450: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 16:57:23.858: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 16:57:24.445: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 16:57:25.021: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 16:57:25.803: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 16:57:26.560: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 16:57:26.561: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 16:57:26.567: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 16:57:26.567: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 16:57:26.567: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 16:57:26.573: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 16:57:26.573: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 16:57:26.573: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 16:57:26.579: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 16:57:26.579: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 16:57:26.579: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 16:57:26.586: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 16:57:26.586: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 16:57:26.586: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 16:57:26.593: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 16:57:26.593: Processing model [a:g] ** Message: 16:57:26.594: Bootstrapper processing model [affine:global:dna2dna] ** Message: 16:57:26.594: Process optimal [optimal:affine:global:dna2dna] ** Message: 16:57:26.595: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 16:57:27.195: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 16:57:27.963: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:57:28.758: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:57:29.673: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 16:57:29.673: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 16:57:29.680: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 16:57:29.680: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 16:57:29.680: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 16:57:29.688: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 16:57:29.688: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:57:29.688: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:57:29.696: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 16:57:29.696: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:57:29.696: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:57:29.703: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:57:29.704: Bootstrapper processing model [affine:global:protein2protein] ** Message: 16:57:29.704: Process optimal [optimal:affine:global:protein2protein] ** Message: 16:57:29.705: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 16:57:30.221: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 16:57:30.876: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:57:31.574: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:57:32.440: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 16:57:32.440: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 16:57:32.446: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 16:57:32.446: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 16:57:32.446: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 16:57:32.454: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 16:57:32.454: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:57:32.454: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:57:32.461: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 16:57:32.462: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:57:32.462: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:57:32.469: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:57:32.469: Processing model [a:b] ** Message: 16:57:32.470: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 16:57:32.470: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 16:57:32.471: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 16:57:33.126: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 16:57:34.136: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 16:57:35.899: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:57:36.801: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:57:37.687: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 16:57:37.687: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 16:57:37.697: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 16:57:37.697: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 16:57:37.697: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 16:57:37.709: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 16:57:37.709: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 16:57:37.709: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 16:57:37.718: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 16:57:37.718: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:57:37.718: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:57:37.727: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 16:57:37.727: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:57:37.727: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:57:37.735: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:57:37.736: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 16:57:37.736: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 16:57:37.738: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 16:57:38.391: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 16:57:39.326: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 16:57:40.254: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:57:40.942: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:57:41.694: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 16:57:41.694: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 16:57:41.702: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 16:57:41.702: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 16:57:41.702: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 16:57:41.710: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 16:57:41.710: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 16:57:41.710: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 16:57:41.718: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 16:57:41.718: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:57:41.718: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:57:41.726: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 16:57:41.726: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:57:41.726: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:57:41.734: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:57:41.734: Processing model [a:l] ** Message: 16:57:41.734: Bootstrapper processing model [affine:local:dna2dna] ** Message: 16:57:41.734: Process optimal [optimal:affine:local:dna2dna] ** Message: 16:57:41.735: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:57:42.025: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:57:42.486: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:57:42.982: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:57:43.863: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:57:44.855: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:57:44.856: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:57:44.869: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:57:44.869: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:57:44.869: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:57:44.883: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:57:44.883: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:57:44.883: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:57:44.897: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:57:44.897: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:57:44.897: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:57:44.908: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:57:44.908: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:57:44.908: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:57:44.922: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:57:44.924: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 16:57:44.925: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:57:45.603: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:57:46.576: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:57:46.576: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:57:46.588: 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: 16:57:46.588: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:57:46.588: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:57:46.601: 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: 16:57:46.601: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 16:57:46.602: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:57:47.175: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:57:48.025: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:57:48.025: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:57:48.061: 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: 16:57:48.061: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:57:48.061: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:57:48.087: 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: 16:57:48.087: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 16:57:48.089: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:57:49.679: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:57:51.980: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:57:51.981: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:57:51.992: 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: 16:57:51.992: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:57:51.992: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:57:52.005: 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: 16:57:52.005: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 16:57:52.343: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 16:57:52.683: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 16:57:52.683: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 16:57:52.695: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 16:57:52.695: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 16:57:52.695: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 16:57:52.709: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 16:57:52.709: Bootstrapper processing model [affine:local:protein2protein] ** Message: 16:57:52.709: Process optimal [optimal:affine:local:protein2protein] ** Message: 16:57:52.710: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:57:53.058: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:57:53.498: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:57:53.970: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:57:54.723: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:57:55.649: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:57:55.649: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:57:55.661: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:57:55.661: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:57:55.661: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:57:55.673: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:57:55.673: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:57:55.673: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:57:55.686: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:57:55.686: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:57:55.686: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:57:55.698: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:57:55.698: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:57:55.698: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:57:55.710: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:57:55.713: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 16:57:55.714: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:57:56.371: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:57:57.318: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:57:57.318: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:57:57.331: 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: 16:57:57.331: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:57:57.331: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:57:57.345: 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: 16:57:57.345: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 16:57:57.346: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:57:57.898: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:57:58.681: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:57:58.681: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:57:58.696: 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: 16:57:58.696: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:57:58.696: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:57:58.713: 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: 16:57:58.713: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 16:57:58.715: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:58:00.253: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:58:03.194: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:58:03.194: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:58:03.212: 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: 16:58:03.212: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:58:03.212: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:58:03.235: 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: 16:58:03.236: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 16:58:03.651: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 16:58:04.070: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 16:58:04.070: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 16:58:04.094: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 16:58:04.094: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 16:58:04.094: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 16:58:04.124: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 16:58:04.124: Processing model [a:o] ** Message: 16:58:04.124: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 16:58:04.124: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 16:58:04.126: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 16:58:04.922: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 16:58:06.053: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 16:58:07.300: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:58:08.277: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:58:09.413: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 16:58:09.413: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 16:58:09.429: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 16:58:09.429: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 16:58:09.429: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 16:58:09.446: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 16:58:09.446: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 16:58:09.446: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 16:58:09.463: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 16:58:09.463: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:58:09.463: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:58:09.479: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 16:58:09.479: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:58:09.479: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:58:09.495: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:58:09.496: Processing model [e2g] ** Message: 16:58:09.496: Bootstrapper processing model [est2genome] ** Message: 16:58:09.496: Process optimal [optimal:est2genome] ** Message: 16:58:09.498: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c ** Message: 16:58:10.723: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c ** Message: 16:58:12.613: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c ** Message: 16:58:14.201: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 16:58:19.253: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 16:58:26.569: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 16:58:26.570: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o ** Message: 16:58:26.596: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 16:58:26.596: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 16:58:26.596: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o ** Message: 16:58:26.625: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 16:58:26.625: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 16:58:26.625: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o ** Message: 16:58:26.666: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 16:58:26.666: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 16:58:26.666: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 16:58:26.697: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 16:58:26.697: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 16:58:26.697: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 16:58:26.725: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 16:58:26.738: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 16:58:26.745: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:28.804: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:31.992: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:31.992: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:32.010: 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: 16:58:32.010: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:32.010: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:32.030: 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: 16:58:32.030: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 16:58:32.031: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:33.146: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:34.772: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:34.772: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:34.793: 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: 16:58:34.793: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:34.793: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:34.817: 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: 16:58:34.817: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 16:58:34.819: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:36.405: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:38.737: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:38.737: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:38.761: 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: 16:58:38.761: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:38.761: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:38.813: 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: 16:58:38.813: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 16:58:38.815: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:39.922: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:41.431: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:41.431: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:41.450: 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: 16:58:41.450: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:41.450: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:41.470: 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: 16:58:41.470: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 16:58:41.475: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:44.799: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:49.866: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:49.866: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:49.883: 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: 16:58:49.883: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:49.883: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:49.900: 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: 16:58:49.900: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:58:49.902: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:50.927: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:52.325: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:58:52.325: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:58:52.344: 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: 16:58:52.344: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:52.344: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:52.364: 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: 16:58:52.364: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:58:52.368: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:58:57.281: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:58:57.281: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:58:57.298: 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: 16:58:57.298: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 16:58:57.300: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:58:59.161: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:59:02.145: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:59:02.145: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:59:02.173: 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: 16:59:02.174: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:59:02.174: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:59:02.204: 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: 16:59:02.204: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 16:59:02.208: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:59:05.791: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:59:12.041: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:59:12.041: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:59:12.061: 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: 16:59:12.061: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:59:12.061: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:59:12.079: 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: 16:59:12.079: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:59:12.080: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:59:13.018: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:59:14.632: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:59:14.632: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:59:14.652: 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: 16:59:14.652: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:59:14.652: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:59:14.672: 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: 16:59:14.672: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:59:14.676: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:59:18.545: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:59:18.545: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:59:18.565: 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: 16:59:18.565: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 16:59:18.567: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:59:20.817: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:59:23.819: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:59:23.819: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:59:23.838: 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: 16:59:23.838: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:59:23.838: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:59:23.859: 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: 16:59:23.860: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 16:59:24.379: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 16:59:24.932: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:59:24.932: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 16:59:24.955: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:59:24.955: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 16:59:24.955: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 16:59:24.977: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 16:59:24.977: Processing model [ner] ** Message: 16:59:24.977: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 16:59:24.977: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 16:59:24.978: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:59:25.360: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:59:25.902: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:59:26.455: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:59:27.522: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:59:28.506: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:59:28.506: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:59:28.525: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:59:28.525: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:59:28.525: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:59:28.545: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:59:28.545: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:59:28.545: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:59:28.564: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:59:28.565: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:59:28.565: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:59:28.584: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:59:28.584: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:59:28.584: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:59:28.604: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:59:28.608: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:59:28.609: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:59:29.351: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:30.472: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:59:30.472: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:59:30.492: 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: 16:59:30.493: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:30.493: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:30.515: 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: 16:59:30.515: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 16:59:30.516: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:59:31.185: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:32.009: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:59:32.009: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:59:32.032: 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: 16:59:32.032: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:32.032: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:32.057: 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: 16:59:32.057: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:59:32.060: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:59:34.145: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:37.531: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:59:37.531: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:59:37.551: 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: 16:59:37.551: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:37.551: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:37.575: 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: 16:59:37.575: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:59:37.576: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:59:38.350: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:39.433: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:59:39.433: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:59:39.458: 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: 16:59:39.458: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:39.458: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:39.484: 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: 16:59:39.484: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:59:39.488: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:42.667: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:42.667: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:42.721: 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: 16:59:42.721: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:59:42.723: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:59:43.759: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:59:45.164: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:59:45.164: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:59:45.193: 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: 16:59:45.193: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:59:45.193: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:59:45.221: 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: 16:59:45.222: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 16:59:45.541: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 16:59:45.913: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:59:45.913: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 16:59:45.941: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 16:59:45.941: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 16:59:45.941: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 16:59:45.967: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 16:59:45.967: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 16:59:45.967: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 16:59:45.968: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:59:46.347: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:59:46.775: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:59:47.205: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:59:48.019: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:59:49.281: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:59:49.282: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:59:49.341: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:59:49.341: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:59:49.341: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:59:49.368: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:59:49.368: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:59:49.368: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:59:49.394: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:59:49.394: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:59:49.394: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:59:49.422: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:59:49.422: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:59:49.422: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:59:49.451: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:59:49.456: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:59:49.458: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:59:50.331: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:59:51.841: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:59:51.841: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:59:51.917: 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: 16:59:51.917: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:59:51.917: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:59:51.985: 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: 16:59:51.985: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 16:59:51.986: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:59:52.854: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:59:53.938: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:59:53.939: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:59:53.962: 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: 16:59:53.962: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:59:53.962: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:59:53.985: 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: 16:59:53.985: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:59:53.987: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:59:55.965: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:59:59.421: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:59:59.421: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:59:59.445: 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: 16:59:59.445: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:59:59.445: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:59:59.472: 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: 16:59:59.472: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:59:59.473: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 17:00:00.290: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 17:00:01.533: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 17:00:01.533: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 17:00:01.562: 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: 17:00:01.562: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 17:00:01.562: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 17:00:01.590: 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: 17:00:01.590: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 17:00:01.594: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 17:00:04.469: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 17:00:04.469: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 17:00:04.501: 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: 17:00:04.501: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 17:00:04.503: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 17:00:05.500: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 17:00:07.070: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 17:00:07.070: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 17:00:07.096: 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: 17:00:07.096: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 17:00:07.096: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 17:00:07.122: 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: 17:00:07.123: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 17:00:07.397: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 17:00:07.749: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:00:07.749: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 17:00:07.774: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 17:00:07.774: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 17:00:07.774: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 17:00:07.804: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 17:00:07.804: Processing model [p2d] ** Message: 17:00:07.805: Bootstrapper processing model [protein2dna:local] ** Message: 17:00:07.805: Process optimal [optimal:protein2dna:local] ** Message: 17:00:07.805: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 17:00:08.288: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 17:00:08.972: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 17:00:09.684: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 17:00:11.415: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 17:00:13.817: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 17:00:13.817: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 17:00:13.869: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 17:00:13.869: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 17:00:13.869: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 17:00:13.945: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 17:00:13.945: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 17:00:13.945: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 17:00:14.025: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 17:00:14.025: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 17:00:14.025: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 17:00:14.085: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 17:00:14.085: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 17:00:14.085: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 17:00:14.137: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 17:00:14.150: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 17:00:14.152: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 17:00:15.796: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 17:00:18.276: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 17:00:18.276: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 17:00:18.306: 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: 17:00:18.306: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 17:00:18.306: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 17:00:18.332: 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: 17:00:18.332: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 17:00:18.333: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 17:00:19.111: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 17:00:20.661: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 17:00:20.661: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 17:00:20.717: 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: 17:00:20.717: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 17:00:20.717: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 17:00:20.801: 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: 17:00:20.801: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 17:00:20.806: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 17:00:24.162: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 17:00:29.901: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 17:00:29.901: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 17:00:29.964: 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: 17:00:29.964: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 17:00:29.964: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 17:00:29.999: 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: 17:00:30.000: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 17:00:30.466: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 17:00:30.985: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 17:00:30.985: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 17:00:31.029: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 17:00:31.029: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 17:00:31.029: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 17:00:31.097: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 17:00:31.097: Processing model [p2d:b] ** Message: 17:00:31.098: Bootstrapper processing model [protein2dna:bestfit] ** Message: 17:00:31.098: Process optimal [optimal:protein2dna:bestfit] ** Message: 17:00:31.101: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 17:00:34.413: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 17:00:39.093: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 17:00:42.640: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 17:00:46.536: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 17:00:49.493: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 17:00:49.493: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 17:00:49.565: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 17:00:49.565: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 17:00:49.565: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 17:00:49.613: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 17:00:49.613: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 17:00:49.613: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 17:00:49.665: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 17:00:49.665: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 17:00:49.665: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 17:00:49.721: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 17:00:49.721: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 17:00:49.722: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 17:00:49.777: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 17:00:49.777: Processing model [p2g] ** Message: 17:00:49.778: Bootstrapper processing model [protein2genome:local] ** Message: 17:00:49.778: Process optimal [optimal:protein2genome:local] ** Message: 17:00:49.780: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 17:00:51.757: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 17:00:54.708: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 17:00:57.464: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 17:01:05.948: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 17:01:18.041: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 17:01:18.041: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 17:01:18.121: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 17:01:18.121: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 17:01:18.121: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 17:01:18.209: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 17:01:18.209: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 17:01:18.209: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 17:01:18.293: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 17:01:18.293: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 17:01:18.293: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 17:01:18.342: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 17:01:18.342: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 17:01:18.342: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 17:01:18.434: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 17:01:18.475: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 17:01:18.482: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:01:25.778: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:01:37.605: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:01:37.605: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:01:37.638: 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: 17:01:37.639: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:01:37.639: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:01:37.675: 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: 17:01:37.675: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 17:01:37.679: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:01:40.606: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:01:46.080: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:01:46.080: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:01:46.111: 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: 17:01:46.111: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:01:46.111: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:01:46.140: 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: 17:01:46.140: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 17:01:46.148: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:02:00.534: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:02:28.278: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:02:28.278: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:02:28.311: 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: 17:02:28.311: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:02:28.312: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:02:28.347: 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: 17:02:28.347: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 17:02:28.350: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:02:31.538: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:02:36.045: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:02:36.045: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:02:36.081: 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: 17:02:36.081: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:02:36.081: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:02:36.117: 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: 17:02:36.117: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 17:02:36.125: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:03:07.549: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:03:07.549: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:03:07.602: 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: 17:03:07.602: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:03:07.612: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:03:16.748: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:03:29.359: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:03:29.359: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:03:29.395: 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: 17:03:29.395: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:03:29.395: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:03:29.434: 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: 17:03:29.434: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 17:03:29.438: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:03:32.498: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:03:37.369: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:03:37.370: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:03:37.415: 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: 17:03:37.416: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:03:37.416: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:03:37.456: 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: 17:03:37.457: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 17:03:37.471: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:03:59.922: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:03:59.922: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:03:59.956: 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: 17:03:59.956: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:03:59.963: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:04:08.927: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:04:24.077: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:04:24.077: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:04:24.145: 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: 17:04:24.145: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:04:24.145: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:04:24.201: 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: 17:04:24.201: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 17:04:24.205: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:04:28.051: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:04:32.697: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:04:32.697: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:04:32.769: 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: 17:04:32.769: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:04:32.769: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:04:32.846: 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: 17:04:32.846: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 17:04:32.873: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:04:56.627: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:04:56.627: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:04:56.664: 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: 17:04:56.664: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:04:56.670: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 17:05:02.254: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 17:05:12.800: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 17:05:12.800: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 17:05:12.840: 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: 17:05:12.840: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 17:05:12.840: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 17:05:12.881: 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: 17:05:12.883: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 17:05:13.418: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 17:05:14.051: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:05:14.052: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 17:05:14.091: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 17:05:14.091: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 17:05:14.092: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 17:05:14.131: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 17:05:14.131: Processing model [p2g:b] ** Message: 17:05:14.132: Bootstrapper processing model [protein2genome:bestfit] ** Message: 17:05:14.132: Process optimal [optimal:protein2genome:bestfit] ** Message: 17:05:14.140: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 17:05:21.084: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 17:05:34.565: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 17:05:42.639: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 17:05:48.357: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 17:05:55.885: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 17:05:55.885: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 17:05:55.923: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 17:05:55.923: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 17:05:55.923: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 17:05:55.966: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 17:05:55.966: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 17:05:55.966: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 17:05:56.005: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 17:05:56.005: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 17:05:56.005: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 17:05:56.043: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 17:05:56.043: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 17:05:56.043: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 17:05:56.090: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 17:05:56.090: Processing model [c2c] ** Message: 17:05:56.091: Bootstrapper processing model [coding2coding] ** Message: 17:05:56.091: Process optimal [optimal:coding2coding] ** Message: 17:05:56.094: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c ** Message: 17:05:57.211: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c ** Message: 17:05:59.284: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c ** Message: 17:06:01.223: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 17:06:05.715: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 17:06:10.886: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 17:06:10.886: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o ** Message: 17:06:10.927: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 17:06:10.927: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 17:06:10.927: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o ** Message: 17:06:10.966: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 17:06:10.966: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 17:06:10.966: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o ** Message: 17:06:11.008: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 17:06:11.008: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 17:06:11.008: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 17:06:11.048: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 17:06:11.048: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 17:06:11.049: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 17:06:11.090: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 17:06:11.114: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 17:06:11.118: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 17:06:14.423: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 17:06:20.493: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 17:06:20.493: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 17:06:20.533: 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: 17:06:20.533: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 17:06:20.533: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 17:06:20.574: 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: 17:06:20.574: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 17:06:20.576: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 17:06:22.221: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 17:06:24.960: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 17:06:24.961: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 17:06:25.002: 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: 17:06:25.002: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 17:06:25.002: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 17:06:25.043: 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: 17:06:25.044: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 17:06:25.050: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 17:06:31.611: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 17:06:44.355: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 17:06:44.355: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 17:06:44.397: 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: 17:06:44.397: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 17:06:44.397: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 17:06:44.440: 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: 17:06:44.441: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 17:06:44.801: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 17:06:45.185: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 17:06:45.185: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 17:06:45.232: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 17:06:45.232: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 17:06:45.232: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 17:06:45.274: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 17:06:45.274: Processing model [c2g] ** Message: 17:06:45.275: Bootstrapper processing model [coding2genome] ** Message: 17:06:45.275: Process optimal [optimal:coding2genome] ** Message: 17:06:45.279: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c ** Message: 17:06:48.588: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c ** Message: 17:06:54.627: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c ** Message: 17:06:59.390: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 17:07:24.265: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 17:08:04.201: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 17:08:04.201: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o ** Message: 17:08:04.248: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 17:08:04.248: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 17:08:04.248: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o ** Message: 17:08:04.296: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 17:08:04.296: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 17:08:04.296: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o ** Message: 17:08:04.346: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 17:08:04.346: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 17:08:04.346: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 17:08:04.391: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 17:08:04.391: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 17:08:04.391: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 17:08:04.440: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 17:08:04.441: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 17:08:05.083: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 17:08:05.817: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:08:05.817: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 17:08:05.865: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 17:08:05.865: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 17:08:05.865: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 17:08:05.922: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 17:08:05.923: Processing model [cd2g] ** Message: 17:08:05.925: Bootstrapper processing model [cdna2genome] ** Message: 17:08:05.925: Process optimal [optimal:cdna2genome] ** Message: 17:08:05.935: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c ** Message: 17:08:18.334: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c ** Message: 17:08:42.383: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c ** Message: 17:09:00.334: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 17:10:27.686: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 17:14:45.001: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 17:14:45.001: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o ** Message: 17:14:45.093: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 17:14:45.093: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 17:14:45.093: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o ** Message: 17:14:45.177: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 17:14:45.177: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 17:14:45.177: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o ** Message: 17:14:45.248: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 17:14:45.248: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 17:14:45.248: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 17:14:45.318: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 17:14:45.318: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 17:14:45.318: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 17:14:45.397: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 17:14:45.399: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 17:14:46.828: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 17:14:48.292: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:14:48.292: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 17:14:48.351: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 17:14:48.352: Adding: [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 17:14:48.352: Adding object file [/build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 17:14:48.413: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 17:14:48.414: Compiling with: [gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/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/x86_64-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 17:14:48.774: Adding: [c4_model_lookup.o] ** Message: 17:14:48.774: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 17:14:48.835: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 17:14:48.920: Done ** Message: 17:14:48.920: 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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate.o exonerate.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ipcress.o ipcress.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate-server.o exonerate-server.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 gchar* g_strup (gchar *string); ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasoftmask.o fastasoftmask.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasplit.o fastasplit.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasubseq.o fastasubseq.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastatranslate.o fastatranslate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastavalidcds.o fastavalidcds.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fasta2esd.o fasta2esd.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaannotatecdna.o fastaannotatecdna.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o esd2esi.o esd2esi.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] 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:163:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/exonerate-2.4.0/src' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/src' make[2]: Leaving directory '/build/exonerate-2.4.0/src' Making all in test make[2]: Entering directory '/build/exonerate-2.4.0/test' Making all in data make[3]: Entering 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 fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j16 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_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/exonerate/usr/bin/fastaremove debian/exonerate/usr/bin/fastafetch debian/exonerate/usr/bin/fastatranslate debian/exonerate/usr/bin/exonerate-server debian/exonerate/usr/bin/fastaannotatecdna debian/exonerate/usr/bin/fastalength debian/exonerate/usr/bin/fastaoverlap debian/exonerate/usr/bin/fastachecksum debian/exonerate/usr/bin/fastadiff debian/exonerate/usr/bin/fastaclean debian/exonerate/usr/bin/esd2esi debian/exonerate/usr/bin/fastasubseq debian/exonerate/usr/bin/fastanrdb debian/exonerate/usr/bin/fastarevcomp debian/exonerate/usr/bin/fastacomposition debian/exonerate/usr/bin/fastaclip debian/exonerate/usr/bin/ipcress debian/exonerate/usr/bin/fastavalidcds debian/exonerate/usr/bin/exonerate debian/exonerate/usr/bin/fasta2esd debian/exonerate/usr/bin/fastareformat debian/exonerate/usr/bin/fastasort debian/exonerate/usr/bin/fastaindex debian/exonerate/usr/bin/fastahardmask debian/exonerate/usr/bin/fastasplit debian/exonerate/usr/bin/fastasoftmask debian/exonerate/usr/bin/fastaexplode were not linked against libgthread-2.0.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'exonerate' in '../exonerate_2.4.0-4_amd64.deb'. dpkg-deb: building package 'exonerate-dbgsym' in '../exonerate-dbgsym_2.4.0-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../exonerate_2.4.0-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2674292 and its subdirectories I: Current time: Tue Jan 3 17:15:16 -12 2023 I: pbuilder-time-stamp: 1672809316