Wed May 15 09:23:34 UTC 2024 I: starting to build exonerate/unstable/amd64 on jenkins on '2024-05-15 09:23' Wed May 15 09:23:34 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_15/20769/console.log Wed May 15 09:23:34 UTC 2024 I: Downloading source for unstable/exonerate=2.4.0-5 --2024-05-15 09:23:34-- http://deb.debian.org/debian/pool/main/e/exonerate/exonerate_2.4.0-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2109 (2.1K) [text/prs.lines.tag] Saving to: ‘exonerate_2.4.0-5.dsc’ 0K .. 100% 296M=0s 2024-05-15 09:23:34 (296 MB/s) - ‘exonerate_2.4.0-5.dsc’ saved [2109/2109] Wed May 15 09:23:34 UTC 2024 I: exonerate_2.4.0-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: exonerate Binary: exonerate Architecture: any Version: 2.4.0-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/exonerate Vcs-Git: https://salsa.debian.org/med-team/exonerate.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libglib2.0-dev, libreadline-dev Package-List: exonerate deb science optional arch=any Checksums-Sha1: 5b119c0aef0fa08c3f4a11014544f2ac5ca8afde 520899 exonerate_2.4.0.orig.tar.gz 69da719216a39755b5ec11dfffda0c32d9ab39f9 9192 exonerate_2.4.0-5.debian.tar.xz Checksums-Sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 520899 exonerate_2.4.0.orig.tar.gz 8008e0266c3af10809bbb8e5de6f9774dcfa413da192bdfa79bad56098762b92 9192 exonerate_2.4.0-5.debian.tar.xz Files: 126fbade003b80b663a1d530c56f1904 520899 exonerate_2.4.0.orig.tar.gz c553b6e4a4b7140f63e052eac3db6be3 9192 exonerate_2.4.0-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/JVhoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF8NQ//URedP/UV7WUNn4jFaiX2Hk2IYgVv9+LE X/ajlGjg9BQoD28Q9FwiRkJCj4GgneI9bBC77ai2zTYOyrcTbDXAim/zlkPa21hF GZioVEj04kgQkd0OVjbjwqF6fpvrmv5C5ntB50uG3bM62SBUQ6Cc2z8nQ802ruN8 HkhCqAJfSiwNuYoRSN0OBKdVkWlswl7/Rzo/Sw7F0fsrsJS6XGxARGKCCvkhMhqc hsu9nHSmrSdNPnLJi7X/ptzs1fliHvrG/WvpykmhckQvJ5YUDEJKgEhkiMvEmmMA 9hDVih0wrVwbW3au+9iTwfZ3tGhSf2On4wUxqD5X3TRJa+OnDNTRq1JjHUATTV8V +AAAXNB6P3G9ky/agmRp4OGMB1sIchjQ4tHntEp6ciZkkWQcV9dxsR/Qo8+E7O4P 42ox50icCJhcB47gN+L7BglktpbvVwptbcd4B0fPffvFEKk6SN1w3JxNzNkXOfJU 5mdb9voQBdhacH/07UascttkitwlBUDW9OjqktpSUWgw4EuEiyZQM+qPyMVSQPMr eT8kEjqtY3YEuqI1X4OaHZjTKIdEZGKfm3U/63eIYwG7yT4CIFSdi8D907rYnKZV EuT/3bbKDWEwVpl5rCGScfYYr38vVYFE6tJFFXxSQk9upjTmaqHR5gV/PiiEziPM Gz8ayBTTCbw= =TFtD -----END PGP SIGNATURE----- Wed May 15 09:23:34 UTC 2024 I: Checking whether the package is not for us Wed May 15 09:23:34 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed May 15 09:23:34 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed May 15 09:52:09 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 14 21:23:36 -12 2024 I: pbuilder-time-stamp: 1715765016 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [exonerate_2.4.0-5.dsc] I: copying [./exonerate_2.4.0.orig.tar.gz] I: copying [./exonerate_2.4.0-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 3 21:18:18 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./exonerate_2.4.0-5.dsc: no acceptable signature found dpkg-source: info: extracting exonerate in exonerate-2.4.0 dpkg-source: info: unpacking exonerate_2.4.0.orig.tar.gz dpkg-source: info: unpacking exonerate_2.4.0-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build-as-needed.patch dpkg-source: info: applying manpages.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpagesyntax.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/665783/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='98853a9e73c84b04bfa9f7b8114eb1c5' 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='665783' 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/r-b-build.SVC8OE52/pbuilderrc_Tkvg --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/b1 --logfile b1/build.log exonerate_2.4.0-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/665783/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19701 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however: Package libglib2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpkgconf3{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline-dev{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsub-override-perl{a} libsysprof-capture-4-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3-packaging{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} uuid-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 33.6 MB of archives. After unpacking 139 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.1-1 [43.9 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.1-1 [200 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.80.2-1 [136 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.80.2-1 [1265 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.80.2-1 [123 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.80.2-1 [170 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.5-2+b1 [351 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.5-2+b2 [158 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.1-1 [25.9 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 46.0-1 [47.1 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.80.2-1 [1741 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2 [349 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-4 [152 kB] Fetched 33.6 MB in 7s (4527 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19701 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20017 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21009 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/exonerate-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../exonerate_2.4.0-5_source.changes dpkg-buildpackage: info: source package exonerate dpkg-buildpackage: info: source version 2.4.0-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' dh_auto_clean rm -rf codegen make[1]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' dh_autoreconf --as-needed autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:773: AM_INIT_AUTOMAKE is expanded from... configure.in:8: the top level configure.in:17: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:17: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:17: the top level configure.in:82: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:82: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.in:82: the top level configure.in:82: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.in:82: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2823: _AC_COMPILE_IFELSE is expanded from... ./lib/autoconf/general.m4:2839: AC_COMPILE_IFELSE is expanded from... ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.in:82: the top level configure.in:315: warning: AC_OUTPUT should be used without arguments. configure.in:315: You should run autoupdate. 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/reproducible-path/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-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking 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 for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for limits.h... yes checking for errno.h... yes checking for math.h... yes checking for strings.h... (cached) yes checking for ctype.h... yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) 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/reproducible-path/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile config.status: executing depfiles commands dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' Making all in doc make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' Making all in man make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man' Making all in man1 make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc' Making all in src make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src' Making all in struct make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sparsecache.o sparsecache.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.test.o bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.o bitarray.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.test.o splaytree.test.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:95, from rangetree.h:23, from rangetree.c:18: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | fread(ba->data, sizeof(guchar), size, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitarray.c: In function 'BitArray_read_int': bitarray.c:189:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(&num, sizeof(guint64), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.o splaytree.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.test.o noitree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.o noitree.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o matrix.test matrix.test.o matrix.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/struct' Making all in general make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/general' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.test.o socket.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.o socket.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.test.o jobqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.o jobqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.test.o threadref.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.o threadref.c socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 169 | g_string_sprintfa(full_msg, "%s", msg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from socket.h:23, from socket.c:31: socket.c: In function 'SocketConnection_read': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:142:9: note: in expansion of macro 'g_string_free' 142 | g_string_free(string, FALSE); | ^~~~~~~~~~~~~ jobqueue.test.c: In function 'main': jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol 34 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 35 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:115, from jobqueue.h:23, from jobqueue.test.c:17: /usr/include/glib-2.0/glib/deprecated/gthread.h:271:10: note: declared here 271 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 138 | if(!g_strcasecmp(arg_string, true_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 140 | if(!g_strcasecmp(arg_string, false_string[i])) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c: In function 'Argument_show_version': argument.c:173:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 173 | g_print("Built on %s\n", __DATE__); | ^~~~~~~~ argument.c: In function 'main': argument.c:306:13: warning: Deprecated pre-processor symbol 306 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 307 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:115: /usr/include/glib-2.0/glib/deprecated/gthread.h:271:10: note: declared here 271 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 502 | g_tree_traverse(arg->option_registry, Argument_set_env_var_func, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:95: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 559 | g_tree_traverse(arg->option_registry, | ^~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lineparse.test lineparse.test.o lineparse.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/general' Making all in sequence make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.test.o submat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.o submat.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splice.test.o splice.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.test.o alphabet.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.test.o codonsubmat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.o codonsubmat.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:95, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 195 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 203 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 317 | if(!g_strcasecmp(name, dna_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 320 | if(!g_strcasecmp(name, protein_string[i])) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 323 | if(!g_strcasecmp(name, unknown_string[i])) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o submat.test submat.test.o submat.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/sequence' Making all in comparison make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.test.o pcr.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.o pcr.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.test.o comparison.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.o comparison.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o match.test.o match.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.test.o seeder.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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] 637 | g_strdown(query_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 638 | g_strdown(target_str); | ^~~~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 640 | g_strup(query_str); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 641 | g_strup(target_str); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | 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] 31 | pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:110, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 59 | register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, | ^~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 69 | g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); | ^~~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 155 | register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, | ^~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 174 | g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); | ^~~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 252 | g_strup(pcr_primer->forward); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56: /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 253 | g_strup(pcr_primer->revcomp); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 357 | pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", | ^~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 363 | pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", | ^~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 366 | pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", | ^~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 381 | g_mem_chunk_destroy(pcr->sensor_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 383 | g_mem_chunk_destroy(pcr->probe_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 384 | g_mem_chunk_destroy(pcr->match_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | 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] 268 | if(!g_strcasecmp(force_fsm, "none")) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 273 | if(!g_strcasecmp(force_fsm, "normal")) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 275 | if(!g_strcasecmp(force_fsm, "compact")) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/comparison' Making all in database make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o index.o index.c In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from fastadb.h:24, from fastadb.c:26: fastadb.c: In function 'FastaDB_Key_get_def': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastadb.c:560:5: note: in expansion of macro 'g_string_free' 560 | g_string_free(s, FALSE); | ^~~~~~~~~~~~~ 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=] 305 | g_print("Sequence Dataset:\n" | ^~~~~~~~~~~~~~~~~~~~~ ...... 316 | dataset->header->number_of_seqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | guint64 {aka long unsigned int} dataset.c:310:39: note: format string is defined here 310 | " number of sequences: %lld\n" | ~~~^ | | | long long int | %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=] 305 | g_print("Sequence Dataset:\n" | ^~~~~~~~~~~~~~~~~~~~~ ...... 317 | dataset->header->max_seq_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | guint64 {aka long unsigned int} dataset.c:311:39: note: format string is defined here 311 | " longest sequence: %lld\n\n", | ~~~^ | | | long long int | %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] 943 | fread(index->dataset_path, sizeof(gchar), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 944 | index->header->dataset_path_len, index->fp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/database' Making all in c4 make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codegen.o codegen.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o optimal.test.o optimal.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.o layout.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.o viterbi.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.o subopt.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.o cgutil.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.test.o layout.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.test.o viterbi.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.test.o opair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.o opair.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.test.o subopt.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.test.o cgutil.test.c In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from codegen.h:23, from codegen.c:23: codegen.c: In function 'Codegen_clean_path_component': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codegen.c:55:5: note: in expansion of macro 'g_string_free' 55 | g_string_free(file_name_str, FALSE); | ^~~~~~~~~~~~~ codegen.c: In function 'Codegen_expand_format': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codegen.c:154:5: note: in expansion of macro 'g_string_free' 154 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 660 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 667 | g_strdown(tg_seq_string); | ^~~~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 677 | g_strdown(qy_seq_string); | ^~~~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 690 | g_strdown(tg_seq_string); | ^~~~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:275:23: note: declared here 275 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 988 | g_strup(tg_codon); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from c4.h:23, from c4.c:16: c4.c: In function 'break_string': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c4.c:1236:5: note: in expansion of macro 'g_string_free' 1236 | g_string_free(s, FALSE); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from viterbi.h:23, from viterbi.c:17: viterbi.c: In function 'Viterbi_expand_macro': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ viterbi.c:965:5: note: in expansion of macro 'g_string_free' 965 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/c4' Making all in bsdp make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/bsdp' Making all in sdp make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.test.o boundary.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.test.o scheduler.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.test.o straceback.test.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/sdp' Making all in model make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.test.o modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.o modeltype.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bootstrapper.o bootstrapper.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 124 | if(!g_strcasecmp(short_name[i], str)) | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/model' Making all in hub make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o analysis.o analysis.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.o bsam.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.test.o bsam.test.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 68 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:95: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, | ^~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 329 | if(!g_strcasecmp(force_scan, "none")){ | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 336 | } else if((!g_strcasecmp(force_scan, "query")) | ^ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 337 | || (!g_strcasecmp(force_scan, "q"))){ | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 339 | } else if((!g_strcasecmp(force_scan, "target")) | ^ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 340 | || (!g_strcasecmp(force_scan, "t"))){ | ^~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c: In function 'Analysis_Client_send': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ analysis.c:474:5: note: in expansion of macro 'g_string_free' 474 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/hub' Making all in program make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' ../../src/model/bootstrapper --compiled no ** Message: 21:26:04.862: Starting building bootstrapping components ** Message: 21:26:04.862: Processing model [u] ** Message: 21:26:04.863: Bootstrapper processing model [ungapped:dna2dna] ** Message: 21:26:04.869: Process optimal [optimal:ungapped:dna2dna] ** (process:679832): WARNING **: 21:26:04.870: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] ** (process:679832): WARNING **: 21:26:04.873: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] ** (process:679832): WARNING **: 21:26:04.873: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] ** (process:679832): WARNING **: 21:26:04.873: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] ** Message: 21:26:04.873: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 21:26:05.270: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 21:26:05.695: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 21:26:06.054: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:26:06.730: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:26:07.413: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 21:26:07.414: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 21:26:07.441: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 21:26:07.442: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 21:26:07.442: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 21:26:07.481: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 21:26:07.482: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 21:26:07.482: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 21:26:07.509: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 21:26:07.510: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:26:07.510: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:26:07.537: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 21:26:07.538: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:26:07.538: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:26:07.569: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:26:07.570: Bootstrapper processing model [ungapped:protein2protein] ** Message: 21:26:07.570: Process optimal [optimal:ungapped:protein2protein] ** Message: 21:26:07.570: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 21:26:08.010: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 21:26:08.450: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 21:26:08.858: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 21:26:09.339: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 21:26:09.871: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 21:26:09.871: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 21:26:09.898: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 21:26:09.898: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 21:26:09.898: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 21:26:09.930: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 21:26:09.930: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 21:26:09.930: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 21:26:09.946: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 21:26:09.946: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 21:26:09.946: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 21:26:09.985: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 21:26:09.986: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 21:26:09.986: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 21:26:09.997: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 21:26:09.998: Bootstrapper processing model [ungapped:dna2protein] ** Message: 21:26:09.998: Process optimal [optimal:ungapped:dna2protein] ** Message: 21:26:09.999: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 21:26:10.490: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 21:26:11.037: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 21:26:11.719: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 21:26:12.498: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 21:26:13.453: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 21:26:13.454: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 21:26:13.475: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 21:26:13.475: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 21:26:13.475: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 21:26:13.494: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 21:26:13.494: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 21:26:13.494: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 21:26:13.507: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 21:26:13.508: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 21:26:13.508: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 21:26:13.527: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 21:26:13.527: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 21:26:13.528: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 21:26:13.542: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 21:26:13.543: Bootstrapper processing model [ungapped:protein2dna] ** Message: 21:26:13.543: Process optimal [optimal:ungapped:protein2dna] ** Message: 21:26:13.544: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 21:26:13.987: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 21:26:14.495: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 21:26:15.091: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 21:26:16.246: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 21:26:17.305: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 21:26:17.306: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 21:26:17.317: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 21:26:17.318: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 21:26:17.319: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 21:26:17.358: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 21:26:17.358: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 21:26:17.358: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 21:26:17.394: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 21:26:17.394: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 21:26:17.395: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 21:26:17.445: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 21:26:17.446: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 21:26:17.446: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 21:26:17.461: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 21:26:17.461: Processing model [u:t] ** Message: 21:26:17.462: Bootstrapper processing model [ungapped:codon] ** Message: 21:26:17.462: Process optimal [optimal:ungapped:codon] ** Message: 21:26:17.463: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 21:26:18.088: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 21:26:19.311: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 21:26:20.554: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 21:26:22.011: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 21:26:23.601: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 21:26:23.602: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 21:26:23.669: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 21:26:23.670: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 21:26:23.670: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 21:26:23.717: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 21:26:23.718: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 21:26:23.719: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 21:26:23.762: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 21:26:23.762: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 21:26:23.762: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 21:26:23.802: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 21:26:23.802: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 21:26:23.802: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 21:26:23.849: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 21:26:23.850: Processing model [a:g] ** Message: 21:26:23.850: Bootstrapper processing model [affine:global:dna2dna] ** Message: 21:26:23.850: Process optimal [optimal:affine:global:dna2dna] ** Message: 21:26:23.851: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 21:26:25.263: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 21:26:26.694: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:26:28.230: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:26:30.197: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 21:26:30.198: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 21:26:30.253: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 21:26:30.254: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 21:26:30.254: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 21:26:30.305: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 21:26:30.306: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:26:30.306: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:26:30.357: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 21:26:30.358: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:26:30.358: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:26:30.417: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:26:30.418: Bootstrapper processing model [affine:global:protein2protein] ** Message: 21:26:30.418: Process optimal [optimal:affine:global:protein2protein] ** Message: 21:26:30.419: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 21:26:31.334: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 21:26:33.383: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 21:26:34.602: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 21:26:36.085: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 21:26:36.085: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 21:26:36.105: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 21:26:36.105: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 21:26:36.105: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 21:26:36.127: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 21:26:36.128: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 21:26:36.129: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 21:26:36.156: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 21:26:36.156: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 21:26:36.156: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 21:26:36.188: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 21:26:36.188: Processing model [a:b] ** Message: 21:26:36.189: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 21:26:36.189: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 21:26:36.190: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 21:26:37.560: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 21:26:39.817: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 21:26:41.246: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:26:42.471: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:26:44.042: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 21:26:44.042: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 21:26:44.086: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 21:26:44.086: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 21:26:44.086: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 21:26:44.132: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 21:26:44.132: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 21:26:44.133: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 21:26:44.157: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 21:26:44.158: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:26:44.158: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:26:44.180: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 21:26:44.180: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:26:44.181: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:26:44.201: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:26:44.202: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 21:26:44.202: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 21:26:44.203: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 21:26:45.349: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 21:26:47.316: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 21:26:49.091: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 21:26:50.360: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 21:26:52.093: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 21:26:52.094: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 21:26:52.188: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 21:26:52.188: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 21:26:52.189: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 21:26:52.273: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 21:26:52.274: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 21:26:52.274: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 21:26:52.321: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 21:26:52.322: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 21:26:52.322: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 21:26:52.355: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 21:26:52.355: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 21:26:52.355: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 21:26:52.379: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 21:26:52.379: Processing model [a:l] ** Message: 21:26:52.379: Bootstrapper processing model [affine:local:dna2dna] ** Message: 21:26:52.379: Process optimal [optimal:affine:local:dna2dna] ** Message: 21:26:52.380: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 21:26:53.014: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 21:26:53.802: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 21:26:54.719: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:26:55.932: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:26:57.189: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 21:26:57.190: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 21:26:57.249: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 21:26:57.250: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 21:26:57.250: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 21:26:57.305: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 21:26:57.306: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 21:26:57.306: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 21:26:57.369: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 21:26:57.370: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:26:57.370: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:26:57.433: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 21:26:57.434: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:26:57.434: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:26:57.489: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:26:57.492: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 21:26:57.493: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:26:58.895: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:27:00.455: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:27:00.455: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:27:00.480: 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: 21:27:00.480: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:27:00.480: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:27:00.506: 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: 21:27:00.506: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 21:27:00.507: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:27:01.411: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:27:02.310: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:27:02.311: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:27:02.338: 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: 21:27:02.339: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:27:02.339: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:27:02.366: 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: 21:27:02.366: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 21:27:02.368: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:27:04.861: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:27:08.473: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:27:08.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:27:08.518: 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: 21:27:08.518: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:27:08.518: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:27:08.554: 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: 21:27:08.555: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 21:27:09.038: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 21:27:09.541: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 21:27:09.542: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 21:27:09.572: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 21:27:09.572: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 21:27:09.573: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 21:27:09.603: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 21:27:09.604: Bootstrapper processing model [affine:local:protein2protein] ** Message: 21:27:09.604: Process optimal [optimal:affine:local:protein2protein] ** Message: 21:27:09.605: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 21:27:10.151: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 21:27:10.926: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 21:27:11.659: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 21:27:12.867: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 21:27:14.574: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 21:27:14.574: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 21:27:14.633: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 21:27:14.634: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 21:27:14.634: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 21:27:14.681: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 21:27:14.682: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 21:27:14.682: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 21:27:14.757: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 21:27:14.758: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 21:27:14.758: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 21:27:14.821: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 21:27:14.821: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 21:27:14.822: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 21:27:14.885: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 21:27:14.888: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 21:27:14.889: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:27:15.655: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:27:17.205: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:27:17.206: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:27:17.277: 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: 21:27:17.278: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:27:17.278: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:27:17.357: 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: 21:27:17.358: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 21:27:17.359: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:27:18.408: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:27:19.630: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:27:19.631: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:27:19.702: 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: 21:27:19.702: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:27:19.702: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:27:19.774: 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: 21:27:19.774: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 21:27:19.776: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:27:22.255: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:27:25.730: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:27:25.730: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:27:25.806: 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: 21:27:25.806: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:27:25.807: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:27:25.905: 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: 21:27:25.907: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 21:27:26.421: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 21:27:26.857: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 21:27:26.858: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 21:27:26.898: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 21:27:26.898: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 21:27:26.898: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 21:27:26.977: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 21:27:26.977: Processing model [a:o] ** Message: 21:27:26.977: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 21:27:26.977: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 21:27:26.978: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 21:27:27.921: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 21:27:29.126: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 21:27:30.381: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:27:31.562: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:27:33.258: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 21:27:33.259: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 21:27:33.353: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 21:27:33.354: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 21:27:33.354: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 21:27:33.395: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 21:27:33.395: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 21:27:33.395: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 21:27:33.434: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 21:27:33.434: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:27:33.434: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:27:34.000: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 21:27:34.000: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:27:34.001: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:27:34.206: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:27:34.207: Processing model [e2g] ** Message: 21:27:34.208: Bootstrapper processing model [est2genome] ** Message: 21:27:34.208: Process optimal [optimal:est2genome] ** Message: 21:27:34.209: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c ** Message: 21:27:37.055: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c ** Message: 21:27:41.106: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c ** Message: 21:27:44.741: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 21:27:50.458: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 21:28:02.124: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 21:28:02.124: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o ** Message: 21:28:02.349: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 21:28:02.349: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 21:28:02.349: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o ** Message: 21:28:03.176: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 21:28:03.176: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 21:28:03.176: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o ** Message: 21:28:03.558: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 21:28:03.558: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 21:28:03.558: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 21:28:03.718: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 21:28:03.718: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 21:28:03.718: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 21:28:03.966: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 21:28:03.983: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 21:28:03.985: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:07.388: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:13.330: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:13.330: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:13.621: 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: 21:28:13.622: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:13.622: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:13.705: 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: 21:28:13.706: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 21:28:13.707: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:16.039: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:20.070: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:20.070: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:20.425: 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: 21:28:20.426: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:20.426: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:20.853: 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: 21:28:20.854: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 21:28:21.102: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:25.060: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:31.058: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:31.058: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:31.237: 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: 21:28:31.238: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:31.238: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:32.577: 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: 21:28:32.578: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 21:28:32.658: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:34.439: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:36.696: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:36.696: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:37.411: 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: 21:28:37.415: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:37.415: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:37.602: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 21:28:37.602: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 21:28:37.614: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:43.962: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:52.133: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:52.134: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:52.661: 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: 21:28:52.662: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:52.662: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:53.389: 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: 21:28:53.390: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 21:28:53.392: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:28:56.287: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:28:59.474: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:28:59.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:28:59.553: 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: 21:28:59.554: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:28:59.554: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:28:59.637: 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: 21:28:59.638: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 21:28:59.641: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:08.481: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:08.482: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:29:08.601: 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: 21:29:08.602: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 21:29:08.607: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:29:11.674: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:18.674: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:29:18.674: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:29:18.802: 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: 21:29:18.802: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:18.802: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:29:18.933: 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: 21:29:18.934: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 21:29:18.948: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:29:25.416: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:35.606: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:29:35.606: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:29:35.665: 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: 21:29:35.665: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:35.665: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:29:35.805: 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: 21:29:35.806: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 21:29:35.807: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:29:37.755: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:41.147: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:29:41.147: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:29:41.557: 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: 21:29:41.558: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:41.558: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:29:41.681: 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: 21:29:41.682: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 21:29:41.685: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:50.293: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:50.294: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:29:50.385: 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: 21:29:50.386: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 21:29:50.388: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 21:29:53.979: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 21:29:59.911: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 21:29:59.911: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 21:29:59.972: 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: 21:29:59.973: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 21:29:59.973: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 21:30:00.042: 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: 21:30:00.044: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 21:30:00.966: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 21:30:01.980: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:30:01.981: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 21:30:02.070: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 21:30:02.070: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 21:30:02.070: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 21:30:02.173: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 21:30:02.174: Processing model [ner] ** Message: 21:30:02.174: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 21:30:02.174: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 21:30:02.175: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 21:30:03.054: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 21:30:04.171: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 21:30:05.152: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 21:30:06.687: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 21:30:08.719: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 21:30:08.719: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 21:30:08.788: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 21:30:08.789: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 21:30:08.789: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 21:30:08.850: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 21:30:08.850: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 21:30:08.850: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 21:30:08.923: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 21:30:08.923: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 21:30:08.924: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 21:30:08.988: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 21:30:08.988: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 21:30:08.988: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 21:30:09.061: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 21:30:09.067: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 21:30:09.069: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:30:10.663: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:12.750: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:30:12.751: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:30:12.830: 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: 21:30:12.830: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:12.830: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:12.969: 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: 21:30:12.970: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 21:30:12.971: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:30:14.247: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:16.009: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:30:16.010: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:30:16.393: 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: 21:30:16.393: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:16.394: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:16.565: 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: 21:30:16.565: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 21:30:16.571: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:30:20.210: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:25.813: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:30:25.815: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:30:25.897: 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: 21:30:25.901: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:25.901: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:25.994: 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: 21:30:25.995: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 21:30:25.996: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:30:27.324: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:29.247: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:30:29.247: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:30:29.336: 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: 21:30:29.336: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:29.336: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:29.398: 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: 21:30:29.399: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 21:30:29.402: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:33.366: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:33.366: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:33.556: 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: 21:30:33.556: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 21:30:33.558: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 21:30:35.120: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 21:30:37.541: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 21:30:37.542: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 21:30:37.598: 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: 21:30:37.599: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 21:30:37.599: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 21:30:37.654: 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: 21:30:37.655: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 21:30:37.989: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 21:30:38.402: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:30:38.403: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 21:30:38.461: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 21:30:38.461: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 21:30:38.461: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 21:30:38.539: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 21:30:38.540: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 21:30:38.540: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 21:30:38.541: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 21:30:38.991: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 21:30:39.849: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 21:30:40.669: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 21:30:41.924: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 21:30:43.228: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 21:30:43.229: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 21:30:43.297: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 21:30:43.298: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 21:30:43.298: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 21:30:43.367: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 21:30:43.367: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 21:30:43.367: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 21:30:43.457: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 21:30:43.458: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 21:30:43.458: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 21:30:43.510: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 21:30:43.511: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 21:30:43.511: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 21:30:43.574: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 21:30:43.578: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 21:30:43.579: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:30:44.795: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:30:46.186: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:30:46.186: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:30:46.247: 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: 21:30:46.248: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:30:46.248: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:30:46.307: 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: 21:30:46.307: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 21:30:46.324: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:30:47.322: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:30:48.787: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:30:48.787: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:30:48.852: 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: 21:30:48.852: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:30:48.852: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:30:48.908: 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: 21:30:48.908: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 21:30:48.910: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:30:50.962: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:30:54.108: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:30:54.109: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:30:54.166: 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: 21:30:54.167: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:30:54.167: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:30:54.225: 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: 21:30:54.225: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 21:30:54.251: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:30:55.067: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:30:56.432: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:30:56.432: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:30:56.532: 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: 21:30:56.533: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:30:56.533: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:30:56.611: 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: 21:30:56.611: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 21:30:56.613: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:31:00.593: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:31:00.593: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:31:00.653: 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: 21:31:00.654: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 21:31:00.655: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 21:31:01.884: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 21:31:03.474: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 21:31:03.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 21:31:03.528: 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: 21:31:03.528: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 21:31:03.528: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 21:31:03.584: 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: 21:31:03.585: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 21:31:04.229: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 21:31:04.577: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:31:04.577: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 21:31:04.632: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 21:31:04.632: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 21:31:04.633: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 21:31:04.700: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 21:31:04.700: Processing model [p2d] ** Message: 21:31:04.700: Bootstrapper processing model [protein2dna:local] ** Message: 21:31:04.700: Process optimal [optimal:protein2dna:local] ** Message: 21:31:04.701: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 21:31:05.568: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 21:31:06.595: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 21:31:07.565: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 21:31:09.568: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 21:31:11.912: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 21:31:11.912: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 21:31:11.971: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 21:31:11.972: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 21:31:11.972: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 21:31:12.028: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 21:31:12.029: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 21:31:12.029: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 21:31:12.091: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 21:31:12.091: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 21:31:12.092: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 21:31:12.165: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 21:31:12.166: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 21:31:12.166: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 21:31:12.281: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 21:31:12.289: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 21:31:12.292: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 21:31:14.018: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 21:31:16.410: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 21:31:16.411: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 21:31:16.467: 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: 21:31:16.468: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 21:31:16.468: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 21:31:16.529: 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: 21:31:16.529: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 21:31:16.531: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 21:31:17.588: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 21:31:19.542: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 21:31:19.542: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 21:31:19.598: 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: 21:31:19.599: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 21:31:19.599: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 21:31:19.661: 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: 21:31:19.661: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 21:31:19.664: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 21:31:23.158: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 21:31:28.158: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 21:31:28.158: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 21:31:28.220: 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: 21:31:28.221: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 21:31:28.221: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 21:31:28.608: 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: 21:31:28.609: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 21:31:28.977: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 21:31:29.344: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 21:31:29.344: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 21:31:29.404: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 21:31:29.404: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 21:31:29.405: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 21:31:29.479: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 21:31:29.479: Processing model [p2d:b] ** Message: 21:31:29.479: Bootstrapper processing model [protein2dna:bestfit] ** Message: 21:31:29.480: Process optimal [optimal:protein2dna:bestfit] ** Message: 21:31:29.481: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 21:31:31.439: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 21:31:34.655: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 21:31:38.292: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 21:31:40.497: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 21:31:42.855: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 21:31:42.856: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 21:31:42.926: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 21:31:42.927: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 21:31:42.927: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 21:31:43.432: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 21:31:43.432: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 21:31:43.432: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 21:31:43.618: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 21:31:43.618: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 21:31:43.618: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 21:31:43.899: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 21:31:43.899: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 21:31:43.899: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 21:31:44.224: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 21:31:44.224: Processing model [p2g] ** Message: 21:31:44.225: Bootstrapper processing model [protein2genome:local] ** Message: 21:31:44.225: Process optimal [optimal:protein2genome:local] ** Message: 21:31:44.226: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 21:31:46.372: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 21:31:49.473: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 21:31:52.606: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 21:31:59.695: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 21:32:10.480: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 21:32:10.480: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 21:32:10.877: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 21:32:10.877: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 21:32:10.877: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 21:32:11.424: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 21:32:11.424: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 21:32:11.424: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 21:32:11.898: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 21:32:11.898: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 21:32:11.898: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 21:32:12.376: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 21:32:12.376: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 21:32:12.376: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 21:32:12.678: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 21:32:12.708: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 21:32:12.712: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:32:19.459: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:32:31.891: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:32:31.891: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:32:32.204: 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: 21:32:32.205: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:32:32.205: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:32:32.931: 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: 21:32:32.931: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 21:32:32.933: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:32:37.394: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:32:43.975: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:32:43.976: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:32:44.054: 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: 21:32:44.054: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:32:44.054: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:32:44.171: 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: 21:32:44.171: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 21:32:44.178: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:33:00.601: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:33:38.354: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:33:38.354: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:33:38.801: 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: 21:33:38.801: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:33:38.801: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:33:39.169: 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: 21:33:39.169: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 21:33:39.171: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:33:43.669: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:33:50.672: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:33:50.673: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:33:51.383: 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: 21:33:51.384: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:33:51.384: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:33:52.274: 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: 21:33:52.275: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 21:33:52.291: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:34:19.175: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:34:19.176: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:34:19.257: 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: 21:34:19.258: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 21:34:19.262: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:34:26.416: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:34:40.174: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:34:40.175: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:34:40.534: 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: 21:34:40.534: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:34:40.534: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:34:40.748: 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: 21:34:40.749: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 21:34:40.751: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:34:44.819: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:34:51.557: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:34:51.557: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:34:51.918: 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: 21:34:51.918: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:34:51.918: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:34:52.398: 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: 21:34:52.398: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 21:34:52.405: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:35:17.467: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:35:17.467: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:35:17.586: 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: 21:35:17.586: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 21:35:17.591: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:35:25.912: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:35:40.436: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:35:40.436: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:35:40.884: 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: 21:35:40.884: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:35:40.884: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:35:41.349: 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: 21:35:41.349: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 21:35:41.352: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:35:45.683: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:35:52.597: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:35:52.597: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:35:53.101: 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: 21:35:53.102: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:35:53.102: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:35:53.894: 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: 21:35:53.894: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 21:35:53.902: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:36:23.642: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:36:23.642: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:36:24.060: 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: 21:36:24.060: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 21:36:24.064: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 21:36:32.206: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 21:36:47.054: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 21:36:47.054: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 21:36:47.359: 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: 21:36:47.359: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 21:36:47.360: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 21:36:47.540: 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: 21:36:47.542: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 21:36:48.283: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 21:36:48.981: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:36:48.981: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 21:36:49.086: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 21:36:49.086: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 21:36:49.087: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 21:36:49.396: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 21:36:49.397: Processing model [p2g:b] ** Message: 21:36:49.398: Bootstrapper processing model [protein2genome:bestfit] ** Message: 21:36:49.398: Process optimal [optimal:protein2genome:bestfit] ** Message: 21:36:49.404: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 21:36:58.814: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 21:37:18.651: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 21:37:31.016: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 21:37:39.138: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 21:37:50.047: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 21:37:50.047: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 21:37:50.159: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 21:37:50.159: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 21:37:50.159: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 21:37:50.325: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 21:37:50.326: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 21:37:50.326: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 21:37:50.570: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 21:37:50.570: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 21:37:50.570: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 21:37:50.921: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 21:37:50.921: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 21:37:50.921: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 21:37:51.541: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 21:37:51.542: Processing model [c2c] ** Message: 21:37:51.542: Bootstrapper processing model [coding2coding] ** Message: 21:37:51.542: Process optimal [optimal:coding2coding] ** Message: 21:37:51.544: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c ** Message: 21:37:53.160: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c ** Message: 21:37:55.954: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c ** Message: 21:37:59.002: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 21:38:04.849: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 21:38:12.157: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 21:38:12.157: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o ** Message: 21:38:12.334: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 21:38:12.335: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 21:38:12.335: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o ** Message: 21:38:12.799: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 21:38:12.799: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 21:38:12.799: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o ** Message: 21:38:13.490: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 21:38:13.490: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 21:38:13.490: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 21:38:14.193: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 21:38:14.193: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 21:38:14.193: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 21:38:14.635: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 21:38:14.660: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 21:38:14.664: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 21:38:19.326: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 21:38:27.051: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 21:38:27.051: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 21:38:27.248: 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: 21:38:27.249: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 21:38:27.249: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 21:38:27.455: 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: 21:38:27.456: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 21:38:27.457: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 21:38:30.061: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 21:38:33.842: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 21:38:33.843: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 21:38:34.099: 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: 21:38:34.100: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 21:38:34.100: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 21:38:34.317: 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: 21:38:34.317: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 21:38:34.323: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 21:38:45.504: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 21:39:19.698: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 21:39:19.698: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 21:39:19.977: 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: 21:39:19.978: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 21:39:19.978: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 21:39:20.281: 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: 21:39:20.283: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 21:39:21.014: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 21:39:21.990: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 21:39:21.990: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 21:39:22.159: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 21:39:22.159: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 21:39:22.160: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 21:39:22.410: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 21:39:22.411: Processing model [c2g] ** Message: 21:39:22.412: Bootstrapper processing model [coding2genome] ** Message: 21:39:22.412: Process optimal [optimal:coding2genome] ** Message: 21:39:22.417: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c ** Message: 21:39:34.375: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c ** Message: 21:40:06.534: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c ** Message: 21:40:28.230: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 21:40:51.998: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 21:41:42.085: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 21:41:42.086: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o ** Message: 21:41:42.262: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 21:41:42.262: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 21:41:42.262: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o ** Message: 21:41:42.455: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 21:41:42.455: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 21:41:42.456: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o ** Message: 21:41:42.783: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 21:41:42.783: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 21:41:42.784: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 21:41:42.995: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 21:41:42.995: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 21:41:42.995: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 21:41:43.368: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 21:41:43.370: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 21:41:44.025: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 21:41:44.760: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:41:44.760: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 21:41:44.952: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 21:41:44.953: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 21:41:44.953: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 21:41:45.261: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 21:41:45.261: Processing model [cd2g] ** Message: 21:41:45.263: Bootstrapper processing model [cdna2genome] ** Message: 21:41:45.263: Process optimal [optimal:cdna2genome] ** Message: 21:41:45.270: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c ** Message: 21:42:10.376: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c ** Message: 21:43:02.841: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c ** Message: 21:43:49.162: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 21:46:37.609: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 21:50:59.313: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 21:50:59.314: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o ** Message: 21:51:00.529: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 21:51:00.530: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 21:51:00.530: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o ** Message: 21:51:02.485: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 21:51:02.486: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 21:51:02.486: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o ** Message: 21:51:03.433: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 21:51:03.434: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 21:51:03.434: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 21:51:04.989: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 21:51:04.990: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 21:51:04.990: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 21:51:06.657: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 21:51:06.659: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 21:51:08.733: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 21:51:11.141: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 21:51:11.142: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 21:51:12.333: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 21:51:12.334: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 21:51:12.334: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 21:51:13.980: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 21:51:13.981: Compiling with: [gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 21:51:15.261: Adding: [c4_model_lookup.o] ** Message: 21:51:15.262: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 21:51:17.688: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 21:51:19.458: Done ** Message: 21:51:19.459: Finished building bootstrapping components make all-am make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ipcress.o ipcress.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate-server.o exonerate-server.c In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/c4/viterbi.h:23, from ../../src/c4/viterbi.c:17: ../../src/c4/viterbi.c: In function 'Viterbi_expand_macro': /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/c4/viterbi.c:965:5: note: in expansion of macro 'g_string_free' 965 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 354 | g_string_sprintfa(str, " %d %d %d", | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 357 | g_string_sprintfa(str, "\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from exonerate-server.c:19: /usr/include/glib-2.0/glib/gstring.h:74:5: warning: ignoring return value of 'g_string_free_and_steal' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | (__builtin_constant_p (free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | ((free_segment) ? \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | (g_string_free) ((str), (free_segment)) : \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | g_string_free_and_steal (str)) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | : \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 | (g_string_free) ((str), (free_segment))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:366:9: note: in expansion of macro 'g_string_free' 366 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 265 | g_strup(primer_b); | ^~~~~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/reproducible-path/exonerate-2.4.0/src/program' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/program' Making all in util make[3]: Entering directory '/build/reproducible-path/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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaexplode.o fastaexplode.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastafetch.o fastafetch.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaindex.o fastaindex.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastalength.o fastalength.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastanrdb.o fastanrdb.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaoverlap.o fastaoverlap.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastareformat.o fastareformat.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaremove.o fastaremove.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastarevcomp.o fastarevcomp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasoftmask.o fastasoftmask.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasort.o fastasort.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasplit.o fastasplit.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasubseq.o fastasubseq.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastatranslate.o fastatranslate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastavalidcds.o fastavalidcds.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; | ^~~~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fasta2esd.o fasta2esd.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaannotatecdna.o fastaannotatecdna.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o esd2esi.o esd2esi.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(query, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastasort.c: In function 'SortKey_Mask_create': gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 132 | else if(!g_strcasecmp(sort_key, "len")) | ^~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 134 | else if(!g_strcasecmp(sort_key, "seq")) | ^~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] 92 | output_dir, G_DIR_SEPARATOR, g_basename(query_path)); | ^~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:50, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/include/glib-2.0/glib/gfileutils.h:207:14: note: declared here 207 | const gchar *g_basename (const gchar *file_name); | ^~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src' Making all in test make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' Making all in data make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making all in cdna make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' Making all in protein make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making all in exonerate make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' Making all in ipcress make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' Making all in util make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' make[1]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' /usr/bin/make -C test check make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' Making check in data make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making check in cdna make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' Making check in protein make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making check in exonerate make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' /usr/bin/make check-TESTS make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/exonerate' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' Making check in ipcress make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' /usr/bin/make check-TESTS make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/ipcress' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' Making check in util make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/util' /usr/bin/make check-TESTS make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/util' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[1]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/exonerate/ make -j20 install DESTDIR=/build/reproducible-path/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' Making install in doc make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' Making install in man make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man' Making install in man1 make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[5]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' make[5]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/doc/man' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/doc' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/doc' Making install in src make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src' Making install in struct make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/struct' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/struct' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/struct' Making install in general make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/general' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/general' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/general' Making install in sequence make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/sequence' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/sequence' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/sequence' Making install in comparison make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/comparison' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/comparison' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/comparison' Making install in database make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/database' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/database' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/database' Making install in c4 make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/c4' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/c4' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/c4' Making install in bsdp make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/bsdp' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/bsdp' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/bsdp' Making install in sdp make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/sdp' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/sdp' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/sdp' Making install in model make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/model' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/model' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/model' Making install in hub make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/hub' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src/hub' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/hub' Making install in program make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' make install-am make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' make[5]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' /usr/bin/mkdir -p '/build/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/bin' make[5]: Nothing to be done for 'install-data-am'. /usr/bin/install -c exonerate ipcress exonerate-server '/build/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/bin' make[5]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/program' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/program' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/program' Making install in util make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/util' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/util' /usr/bin/mkdir -p '/build/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/bin' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/util' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/src' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src' Making install in test make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' Making install in data make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making install in cdna make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/data/cdna' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/cdna' Making install in protein make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[5]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/data' make[4]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/data' Making install in exonerate make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/exonerate' Making install in ipcress make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/ipcress' Making install in util make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/test' make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0/test' make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/test' make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/exonerate-2.4.0' make[2]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' make[1]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' dh_installchangelogs -k ChangeLog make[1]: Leaving directory '/build/reproducible-path/exonerate-2.4.0' debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' dh_installexamples mkdir -p /build/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples; cp -a test/* /build/reproducible-path/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples/; find /build/reproducible-path/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/reproducible-path/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/reproducible-path/exonerate-2.4.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'exonerate' in '../exonerate_2.4.0-5_amd64.deb'. dpkg-deb: building package 'exonerate-dbgsym' in '../exonerate-dbgsym_2.4.0-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../exonerate_2.4.0-5_amd64.buildinfo dpkg-genchanges --build=binary -O../exonerate_2.4.0-5_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/665783 and its subdirectories I: Current time: Tue May 14 21:52:08 -12 2024 I: pbuilder-time-stamp: 1715766728 Wed May 15 09:52:10 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed May 15 09:52:10 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed May 15 10:09:46 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed May 15 10:09:46 UTC 2024 I: exonerate_2.4.0-5_amd64.changes: Format: 1.8 Date: Thu, 03 Dec 2020 21:56:27 +0100 Source: exonerate Binary: exonerate exonerate-dbgsym Architecture: amd64 Version: 2.4.0-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: exonerate - generic tool for pairwise sequence comparison Changes: exonerate (2.4.0-5) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Update watch file format version to 4. * Set field Upstream-Name in debian/copyright. * Refer to specific version of license GPL-3+. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: 3cb2076141d5cc7de78ed522d26cbba8428cb638 6859620 exonerate-dbgsym_2.4.0-5_amd64.deb 200c488b7948523f5a968c506e151cf369cb41a8 6297 exonerate_2.4.0-5_amd64.buildinfo 725229dc25dcee80e9a5a5864dd7d0c8e63fe441 1961524 exonerate_2.4.0-5_amd64.deb Checksums-Sha256: 979c2a6104d1ecdebc52fc692fbbd44431510337635fe8dd0b4f204096d16014 6859620 exonerate-dbgsym_2.4.0-5_amd64.deb 57901b934457f2b46beaeb2aafcac5361a2fbf1afbbcd02f03734a8a24e9ed72 6297 exonerate_2.4.0-5_amd64.buildinfo 2617af36db97350003e8324946319f97ed8274f0ed15f74a2bac7e84da51bfd5 1961524 exonerate_2.4.0-5_amd64.deb Files: e2806416a0247e7a4d1df18ec0397600 6859620 debug optional exonerate-dbgsym_2.4.0-5_amd64.deb da63f129c3b1179e50ba109448cf68c0 6297 science optional exonerate_2.4.0-5_amd64.buildinfo fad13afea375b6ee9658d7a9e5a6513e 1961524 science optional exonerate_2.4.0-5_amd64.deb Wed May 15 10:09:47 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_15-20769.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/exonerate_2.4.0-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/exonerate_2.4.0-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/exonerate_2.4.0-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/b1/exonerate_2.4.0-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.SVC8OE52/b2/exonerate_2.4.0-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.442s) 0.442s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.106s) 0.106s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 770ms CPU time consumed: 771ms Wed May 15 10:09:49 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 10:09:49 UTC 2024 I: exonerate from unstable built successfully and reproducibly on amd64. Wed May 15 10:09:50 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 10:09:50 UTC 2024 I: Submitting 8.0K b1/exonerate_2.4.0-5_amd64.buildinfo.asc Wed May 15 10:09:51 UTC 2024 I: Submitting 8.0K b2/exonerate_2.4.0-5_amd64.buildinfo.asc Wed May 15 10:09:51 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 10:09:51 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 10:09:51 UTC 2024 I: Removing signed exonerate_2.4.0-5_amd64.buildinfo.asc files: removed './b1/exonerate_2.4.0-5_amd64.buildinfo.asc' removed './b2/exonerate_2.4.0-5_amd64.buildinfo.asc'