Mon May 8 07:01:59 UTC 2023 I: starting to build exonerate/bookworm/arm64 on jenkins on '2023-05-08 07:01' Mon May 8 07:01:59 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_23/28235/console.log Mon May 8 07:01:59 UTC 2023 I: Downloading source for bookworm/exonerate=2.4.0-5 --2023-05-08 07:01:59-- http://cdn-fastly.deb.debian.org/debian/pool/main/e/exonerate/exonerate_2.4.0-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2109 (2.1K) [text/prs.lines.tag] Saving to: ‘exonerate_2.4.0-5.dsc’ 0K .. 100% 156M=0s 2023-05-08 07:01:59 (156 MB/s) - ‘exonerate_2.4.0-5.dsc’ saved [2109/2109] Mon May 8 07:01:59 UTC 2023 I: exonerate_2.4.0-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: exonerate Binary: exonerate Architecture: any Version: 2.4.0-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/exonerate Vcs-Git: https://salsa.debian.org/med-team/exonerate.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libglib2.0-dev, libreadline-dev Package-List: exonerate deb science optional arch=any Checksums-Sha1: 5b119c0aef0fa08c3f4a11014544f2ac5ca8afde 520899 exonerate_2.4.0.orig.tar.gz 69da719216a39755b5ec11dfffda0c32d9ab39f9 9192 exonerate_2.4.0-5.debian.tar.xz Checksums-Sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 520899 exonerate_2.4.0.orig.tar.gz 8008e0266c3af10809bbb8e5de6f9774dcfa413da192bdfa79bad56098762b92 9192 exonerate_2.4.0-5.debian.tar.xz Files: 126fbade003b80b663a1d530c56f1904 520899 exonerate_2.4.0.orig.tar.gz c553b6e4a4b7140f63e052eac3db6be3 9192 exonerate_2.4.0-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/JVhoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF8NQ//URedP/UV7WUNn4jFaiX2Hk2IYgVv9+LE X/ajlGjg9BQoD28Q9FwiRkJCj4GgneI9bBC77ai2zTYOyrcTbDXAim/zlkPa21hF GZioVEj04kgQkd0OVjbjwqF6fpvrmv5C5ntB50uG3bM62SBUQ6Cc2z8nQ802ruN8 HkhCqAJfSiwNuYoRSN0OBKdVkWlswl7/Rzo/Sw7F0fsrsJS6XGxARGKCCvkhMhqc hsu9nHSmrSdNPnLJi7X/ptzs1fliHvrG/WvpykmhckQvJ5YUDEJKgEhkiMvEmmMA 9hDVih0wrVwbW3au+9iTwfZ3tGhSf2On4wUxqD5X3TRJa+OnDNTRq1JjHUATTV8V +AAAXNB6P3G9ky/agmRp4OGMB1sIchjQ4tHntEp6ciZkkWQcV9dxsR/Qo8+E7O4P 42ox50icCJhcB47gN+L7BglktpbvVwptbcd4B0fPffvFEKk6SN1w3JxNzNkXOfJU 5mdb9voQBdhacH/07UascttkitwlBUDW9OjqktpSUWgw4EuEiyZQM+qPyMVSQPMr eT8kEjqtY3YEuqI1X4OaHZjTKIdEZGKfm3U/63eIYwG7yT4CIFSdi8D907rYnKZV EuT/3bbKDWEwVpl5rCGScfYYr38vVYFE6tJFFXxSQk9upjTmaqHR5gV/PiiEziPM Gz8ayBTTCbw= =TFtD -----END PGP SIGNATURE----- Mon May 8 07:01:59 UTC 2023 I: Checking whether the package is not for us Mon May 8 07:01:59 UTC 2023 I: Starting 1st build on remote node codethink14-arm64.debian.net. Mon May 8 07:01:59 UTC 2023 I: Preparing to do remote build '1' on codethink14-arm64.debian.net. Mon May 8 07:42:30 UTC 2023 I: Deleting $TMPDIR on codethink14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 7 19:02:05 -12 2023 I: pbuilder-time-stamp: 1683529325 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 09:18:18 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: 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/16674/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='16674' 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.8I43V6zo/pbuilderrc_O4XF --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/b1 --logfile b1/build.log exonerate_2.4.0-5.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink14-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 22:27 /bin -> usr/bin I: user script /srv/workspace/pbuilder/16674/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: arm64 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 ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however: Package libglib2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libicu72{a} libmagic-mgc{a} libmagic1{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} libreadline8{a} libselinux1-dev{a} libsepol-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} uuid-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 140 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 uuid-dev arm64 2.38.1-5+b1 [40.5 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libblkid-dev arm64 2.38.1-5+b1 [183 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libffi-dev arm64 3.4.4-1 [56.0 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-data all 2.74.6-2 [1207 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-bin arm64 2.74.6-2 [106 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-dev-bin arm64 2.74.6-2 [150 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libsepol-dev arm64 3.4-2 [343 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libpcre2-16-0 arm64 10.42-1 [216 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libpcre2-32-0 arm64 10.42-1 [207 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libpcre2-posix3 arm64 10.42-1 [55.5 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libpcre2-dev arm64 10.42-1 [664 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libselinux1-dev arm64 3.4-1+b5 [159 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libmount-dev arm64 2.38.1-5+b1 [22.5 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-dev arm64 2.74.6-2 [1613 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libncurses-dev arm64 6.4-2 [335 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libreadline-dev arm64 8.2-1.3 [151 kB] Fetched 31.9 MB in 1s (41.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20366 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... 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Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libffi-dev:arm64 (3.4.4-1) ... Setting up libpcre2-16-0:arm64 (10.42-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:arm64 (10.42-1) ... Setting up libglib2.0-data (2.74.6-2) ... Setting up libpkgconf3:arm64 (1.8.1-1) ... Setting up uuid-dev:arm64 (2.38.1-5+b1) ... Setting up libncurses6:arm64 (6.4-2) ... Setting up autopoint (0.21-12) ... Setting up libsepol-dev:arm64 (3.4-2) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libpcre2-posix3:arm64 (10.42-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libblkid-dev:arm64 (2.38.1-5+b1) ... Setting up libncurses-dev:arm64 (6.4-2) ... Setting up gettext (0.21-12) ... Setting up libpcre2-dev:arm64 (10.42-1) ... Setting up libtool (2.4.7-5) ... Setting up libselinux1-dev:arm64 (3.4-1+b5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libglib2.0-bin (2.74.6-2) ... Setting up libreadline-dev:arm64 (8.2-1.3) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libmount-dev:arm64 (2.38.1-5+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up libglib2.0-dev-bin (2.74.6-2) ... Setting up libglib2.0-dev:arm64 (2.74.6-2) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/exonerate-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && 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 arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/exonerate-2.4.0' dh_auto_clean rm -rf codegen make[1]: Leaving directory '/build/exonerate-2.4.0' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/exonerate-2.4.0' dh_autoreconf --as-needed 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/exonerate-2.4.0' dh_auto_configure ./configure --build=aarch64-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/aarch64-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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu Set host to aarch64-unknown-linux-gnu aarch64-unknown-linux-gnu *** Unknown build platform: aarch64-unknown-linux-gnu *** Set source_root_dir to /build/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile config.status: executing depfiles commands dh_auto_build make -j8 make[1]: Entering directory '/build/exonerate-2.4.0' Making all in doc make[2]: Entering directory '/build/exonerate-2.4.0/doc' Making all in man make[3]: Entering directory '/build/exonerate-2.4.0/doc/man' Making all in man1 make[4]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/build/exonerate-2.4.0/doc/man' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/exonerate-2.4.0/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/exonerate-2.4.0/doc' Making all in src make[2]: Entering directory '/build/exonerate-2.4.0/src' Making all in struct make[3]: Entering directory '/build/exonerate-2.4.0/src/struct' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fsm.test.o fsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fsm.o fsm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o recyclebin.o recyclebin.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o matrix.test.o matrix.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o matrix.o matrix.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pqueue.test.o pqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pqueue.o pqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o slist.test.o slist.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o slist.o slist.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o rangetree.test.o rangetree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o rangetree.o rangetree.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o vfsm.test.o vfsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o vfsm.o vfsm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o recyclebin.test.o recyclebin.test.c 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:94, 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, | ^~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sparsecache.test.o sparsecache.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sparsecache.o sparsecache.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o dejavu.test.o dejavu.test.c In file included from /usr/include/glib-2.0/glib.h:64, from vfsm.h:19, from vfsm.c:25: vfsm.c: In function 'VFSM_info': vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 83 | g_message("VFSM info:\n" | ^~~~~~~~~~~~~~ ...... 99 | vfsm->prs, | ~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 83 | g_message("VFSM info:\n" | ^~~~~~~~~~~~~~ ...... 100 | vfsm->prw, | ~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 83 | g_message("VFSM info:\n" | ^~~~~~~~~~~~~~ ...... 101 | vfsm->lrs, | ~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 83 | g_message("VFSM info:\n" | ^~~~~~~~~~~~~~ ...... 102 | vfsm->lrw, | ~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 83 | g_message("VFSM info:\n" | ^~~~~~~~~~~~~~ ...... 103 | vfsm->total | ~~~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:107:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'VFSM_Int' {aka 'long unsigned int'} [-Wformat=] 107 | g_print(" branch_size [%d] [%" VFSM_PRINT_FORMAT "]\n", | ^~~~~~~~~~~~~~~~~~~~~~~ 108 | i, vfsm->branch_size[i]); | ~~~~~~~~~~~~~~~~~~~~ | | | VFSM_Int {aka long unsigned int} gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o dejavu.o dejavu.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.test.o bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.o bitarray.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.test.o splaytree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.o splaytree.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.test.o noitree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.o noitree.c bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | fread(ba->data, sizeof(guchar), size, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitarray.c: In function 'BitArray_read_int': bitarray.c:189:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(&num, sizeof(guint64), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o matrix.test matrix.test.o matrix.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/struct' Making all in general make[3]: Entering directory '/build/exonerate-2.4.0/src/general' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o argument.test.o argument.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o argument.o argument.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o lineparse.test.o lineparse.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o lineparse.o lineparse.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o compoundfile.test.o compoundfile.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o compoundfile.o compoundfile.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.test.o socket.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.o socket.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 138 | if(!g_strcasecmp(arg_string, true_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:114: /usr/include/glib-2.0/glib/deprecated/gthread.h:267:10: note: declared here 267 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function '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:94: /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, | ^~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.test.o jobqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.o jobqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.test.o threadref.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.o threadref.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 jobqueue.test.c: In function 'main': jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol 34 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 35 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:114, from jobqueue.h:23, from jobqueue.test.c:17: /usr/include/glib-2.0/glib/deprecated/gthread.h:267:10: note: declared here 267 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o argument.test argument.test.o argument.o -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/general' Making all in sequence make[3]: Entering directory '/build/exonerate-2.4.0/src/sequence' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sequence.test.o sequence.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sequence.o sequence.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.o alphabet.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o translate.o translate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splice.o splice.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.test.o submat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.o submat.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o translate.test.o translate.test.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:94, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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.h:84, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splice.test.o splice.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.test.o alphabet.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.test.o codonsubmat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.o codonsubmat.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o submat.test submat.test.o submat.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/sequence' Making all in comparison make[3]: Entering directory '/build/exonerate-2.4.0/src/comparison' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o wordhood.test.o wordhood.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o wordhood.o wordhood.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o hspset.test.o hspset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o hspset.o hspset.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o match.o match.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.test.o pcr.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.o pcr.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.test.o comparison.test.c 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:109, 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.h:84: /usr/include/glib-2.0/glib/gstrfuncs.h:212:23: note: declared here 212 | 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:212:23: note: declared here 212 | 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); | ^~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.o comparison.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o match.test.o match.test.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 637 | g_strdown(query_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:84, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | 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:210:23: note: declared here 210 | 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:212:23: note: declared here 212 | 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:212:23: note: declared here 212 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.test.o seeder.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.o seeder.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 268 | if(!g_strcasecmp(force_fsm, "none")) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/comparison' Making all in database make[3]: Entering directory '/build/exonerate-2.4.0/src/database' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastadb.test.o fastadb.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastadb.o fastadb.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastapipe.test.o fastapipe.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastapipe.o fastapipe.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o dataset.test.o dataset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o dataset.o dataset.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o index.test.o index.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o index.o index.c dataset.c: In function 'Dataset_info': dataset.c:305:13: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] 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 In file included from /usr/include/glib-2.0/glib.h:64, from index.h:24, from index.c:21: index.c: In function 'Index_desaturate': index.c:377:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'gint64' {aka 'long int'} [-Wformat=] 377 | g_message("Removed [%" CUSTOM_GUINT64_FORMAT | ^~~~~~~~~~~~ 378 | "] words, [%" CUSTOM_GUINT64_FORMAT "] instances", 379 | removed_words, removed_instances); | ~~~~~~~~~~~~~ | | | gint64 {aka long int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ index.c:377:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'gint64' {aka 'long int'} [-Wformat=] 377 | g_message("Removed [%" CUSTOM_GUINT64_FORMAT | ^~~~~~~~~~~~ 378 | "] words, [%" CUSTOM_GUINT64_FORMAT "] instances", 379 | removed_words, removed_instances); | ~~~~~~~~~~~~~~~~~ | | | gint64 {aka long int} /usr/include/glib-2.0/glib/gmessages.h:350:32: note: in definition of macro 'g_message' 350 | __VA_ARGS__) | ^~~~~~~~~~~ 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/database' Making all in c4 make[3]: Entering directory '/build/exonerate-2.4.0/src/c4' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o region.test.o region.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o region.o region.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o c4.test.o c4.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o c4.o c4.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alignment.test.o alignment.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alignment.o alignment.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codegen.test.o codegen.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codegen.o codegen.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o optimal.test.o optimal.test.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 660 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_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:210:23: note: declared here 210 | 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:210:23: note: declared here 210 | 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:210:23: note: declared here 210 | 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:212:23: note: declared here 212 | 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:212:23: note: declared here 212 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o optimal.o optimal.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.o layout.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.o viterbi.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.o subopt.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.o cgutil.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.test.o layout.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.test.o viterbi.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.test.o opair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.o opair.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.test.o subopt.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.test.o cgutil.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o region.test region.test.o region.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/c4' Making all in bsdp make[3]: Entering directory '/build/exonerate-2.4.0/src/bsdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o heuristic.test.o heuristic.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o heuristic.o heuristic.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsdp.test.o bsdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsdp.o bsdp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o hpair.test.o hpair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o hpair.o hpair.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sar.o sar.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sar.test.o sar.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' Making all in sdp make[3]: Entering directory '/build/exonerate-2.4.0/src/sdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sdp.test.o sdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o sdp.o sdp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.o boundary.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.o scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o lookahead.o lookahead.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.o straceback.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o lookahead.test.o lookahead.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.test.o boundary.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.test.o scheduler.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.test.o straceback.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/sdp' Making all in model make[3]: Entering directory '/build/exonerate-2.4.0/src/model' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o edit_distance.test.o edit_distance.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o edit_distance.o edit_distance.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o affine.test.o affine.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o affine.o affine.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ungapped.o ungapped.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o protein2dna.test.o protein2dna.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o protein2dna.o protein2dna.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o frameshift.o frameshift.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ner.test.o ner.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ner.o ner.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o est2genome.test.o est2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o est2genome.o est2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o intron.o intron.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ungapped.test.o ungapped.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o intron.test.o intron.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o protein2genome.test.o protein2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o protein2genome.o protein2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o phase.o phase.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o coding2coding.test.o coding2coding.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o coding2coding.o coding2coding.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o frameshift.test.o frameshift.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o coding2genome.test.o coding2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o coding2genome.o coding2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cdna2genome.test.o cdna2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cdna2genome.o cdna2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o genome2genome.test.o genome2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o genome2genome.o genome2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o phase.test.o phase.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.test.o modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.o modeltype.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bootstrapper.o bootstrapper.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_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 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/model' Making all in hub make[3]: Entering directory '/build/exonerate-2.4.0/src/hub' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o gam.test.o gam.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o gam.o gam.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o analysis.test.o analysis.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o analysis.o analysis.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.o bsam.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.test.o bsam.test.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 68 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:94: /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, | ^~~~~~~~~~~~~~~ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 329 | if(!g_strcasecmp(force_scan, "none")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 make[3]: Leaving directory '/build/exonerate-2.4.0/src/hub' Making all in program make[3]: Entering directory '/build/exonerate-2.4.0/src/program' ../../src/model/bootstrapper --compiled no ** Message: 19:03:17.525: Starting building bootstrapping components ** Message: 19:03:17.525: Processing model [u] ** Message: 19:03:17.526: Bootstrapper processing model [ungapped:dna2dna] ** Message: 19:03:17.526: Process optimal [optimal:ungapped:dna2dna] ** (process:26212): WARNING **: 19:03:17.526: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:26212): WARNING **: 19:03:17.526: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:26212): WARNING **: 19:03:17.526: Creating codegen directory [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu] ** (process:26212): WARNING **: 19:03:17.526: Creating codegen directory [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu] ** Message: 19:03:17.526: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 19:03:18.026: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 19:03:18.540: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 19:03:19.073: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:03:19.861: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:03:20.665: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 19:03:20.665: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 19:03:20.668: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 19:03:20.668: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 19:03:20.668: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 19:03:20.672: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 19:03:20.672: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 19:03:20.672: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 19:03:20.676: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 19:03:20.676: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:03:20.676: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:03:20.680: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 19:03:20.680: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:03:20.680: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:03:20.684: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:03:20.684: Bootstrapper processing model [ungapped:protein2protein] ** Message: 19:03:20.684: Process optimal [optimal:ungapped:protein2protein] ** Message: 19:03:20.684: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 19:03:21.105: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 19:03:21.590: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 19:03:22.167: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:03:22.897: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:03:23.739: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 19:03:23.739: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 19:03:23.744: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 19:03:23.744: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 19:03:23.744: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 19:03:23.748: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 19:03:23.749: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 19:03:23.749: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 19:03:23.753: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 19:03:23.753: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:03:23.753: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:03:23.757: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 19:03:23.758: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:03:23.758: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:03:23.762: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:03:23.763: Bootstrapper processing model [ungapped:dna2protein] ** Message: 19:03:23.763: Process optimal [optimal:ungapped:dna2protein] ** Message: 19:03:23.763: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 19:03:24.292: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 19:03:24.932: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 19:03:25.669: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 19:03:26.578: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 19:03:27.510: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 19:03:27.510: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 19:03:27.515: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 19:03:27.515: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 19:03:27.515: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 19:03:27.520: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 19:03:27.520: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 19:03:27.520: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 19:03:27.526: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 19:03:27.526: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 19:03:27.526: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 19:03:27.531: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 19:03:27.531: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 19:03:27.531: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 19:03:27.536: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 19:03:27.537: Bootstrapper processing model [ungapped:protein2dna] ** Message: 19:03:27.537: Process optimal [optimal:ungapped:protein2dna] ** Message: 19:03:27.537: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 19:03:28.051: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 19:03:28.644: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 19:03:29.306: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 19:03:30.357: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 19:03:31.266: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 19:03:31.267: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 19:03:31.272: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 19:03:31.272: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 19:03:31.272: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 19:03:31.278: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 19:03:31.278: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 19:03:31.278: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 19:03:31.284: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 19:03:31.284: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 19:03:31.284: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 19:03:31.290: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 19:03:31.290: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 19:03:31.290: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 19:03:31.296: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 19:03:31.296: Processing model [u:t] ** Message: 19:03:31.296: Bootstrapper processing model [ungapped:codon] ** Message: 19:03:31.297: Process optimal [optimal:ungapped:codon] ** Message: 19:03:31.297: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 19:03:32.052: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 19:03:33.026: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 19:03:34.151: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 19:03:35.655: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 19:03:37.072: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 19:03:37.072: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 19:03:37.078: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 19:03:37.079: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 19:03:37.079: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 19:03:37.085: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 19:03:37.085: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 19:03:37.085: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 19:03:37.092: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 19:03:37.092: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 19:03:37.092: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 19:03:37.098: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 19:03:37.099: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 19:03:37.099: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 19:03:37.106: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 19:03:37.106: Processing model [a:g] ** Message: 19:03:37.106: Bootstrapper processing model [affine:global:dna2dna] ** Message: 19:03:37.106: Process optimal [optimal:affine:global:dna2dna] ** Message: 19:03:37.107: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 19:03:38.136: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 19:03:39.525: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:03:40.921: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:03:42.493: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 19:03:42.493: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 19:03:42.501: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 19:03:42.501: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 19:03:42.501: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 19:03:42.508: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 19:03:42.508: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:03:42.508: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:03:42.516: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 19:03:42.516: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:03:42.516: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:03:42.523: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:03:42.524: Bootstrapper processing model [affine:global:protein2protein] ** Message: 19:03:42.524: Process optimal [optimal:affine:global:protein2protein] ** Message: 19:03:42.525: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 19:03:43.531: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 19:03:44.893: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:03:46.272: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:03:47.810: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 19:03:47.810: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 19:03:47.818: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 19:03:47.818: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 19:03:47.818: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 19:03:47.827: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 19:03:47.827: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:03:47.827: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:03:47.835: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 19:03:47.835: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:03:47.835: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:03:47.843: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:03:47.844: Processing model [a:b] ** Message: 19:03:47.844: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 19:03:47.844: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 19:03:47.846: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 19:03:49.182: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 19:03:51.087: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 19:03:52.848: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:03:54.243: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:03:55.807: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 19:03:55.807: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 19:03:55.817: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 19:03:55.817: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 19:03:55.817: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 19:03:55.826: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 19:03:55.826: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 19:03:55.826: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 19:03:55.835: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 19:03:55.835: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:03:55.835: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:03:55.844: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 19:03:55.844: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:03:55.844: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:03:55.854: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:03:55.854: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 19:03:55.854: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 19:03:55.856: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 19:03:57.187: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 19:03:59.141: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 19:04:00.930: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:04:02.357: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:04:03.949: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 19:04:03.949: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 19:04:03.959: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 19:04:03.959: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 19:04:03.959: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 19:04:03.970: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 19:04:03.970: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 19:04:03.970: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 19:04:03.981: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 19:04:03.981: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:04:03.981: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:04:03.992: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 19:04:03.992: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:04:03.992: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:04:04.003: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:04:04.003: Processing model [a:l] ** Message: 19:04:04.003: Bootstrapper processing model [affine:local:dna2dna] ** Message: 19:04:04.003: Process optimal [optimal:affine:local:dna2dna] ** Message: 19:04:04.004: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 19:04:04.611: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 19:04:05.373: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 19:04:06.172: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:04:07.613: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:04:09.265: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 19:04:09.265: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 19:04:09.277: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 19:04:09.277: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 19:04:09.277: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 19:04:09.289: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 19:04:09.289: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 19:04:09.289: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 19:04:09.300: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 19:04:09.300: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:04:09.300: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:04:09.313: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 19:04:09.313: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:04:09.313: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:04:09.325: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:04:09.329: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 19:04:09.330: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:10.553: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:12.313: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:12.313: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:12.325: 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: 19:04:12.325: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:12.325: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:12.338: 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: 19:04:12.338: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 19:04:12.339: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:13.420: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:14.811: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:14.811: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:14.824: 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: 19:04:14.824: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:14.824: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:14.838: 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: 19:04:14.838: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 19:04:14.841: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:17.737: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:22.268: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:22.268: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:22.282: 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: 19:04:22.282: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:22.282: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:22.296: 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: 19:04:22.297: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 19:04:22.942: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 19:04:23.607: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 19:04:23.607: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 19:04:23.621: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 19:04:23.621: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 19:04:23.621: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 19:04:23.635: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 19:04:23.635: Bootstrapper processing model [affine:local:protein2protein] ** Message: 19:04:23.636: Process optimal [optimal:affine:local:protein2protein] ** Message: 19:04:23.636: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 19:04:24.281: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 19:04:25.111: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 19:04:25.987: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:04:27.558: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:04:29.320: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 19:04:29.320: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 19:04:29.335: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 19:04:29.335: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 19:04:29.335: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 19:04:29.350: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 19:04:29.350: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 19:04:29.350: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 19:04:29.365: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 19:04:29.365: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:04:29.365: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:04:29.380: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 19:04:29.380: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:04:29.380: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:04:29.396: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:04:29.399: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 19:04:29.401: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:30.646: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:32.491: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:32.491: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:32.506: 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: 19:04:32.506: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:32.506: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:32.522: 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: 19:04:32.522: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 19:04:32.523: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:33.534: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:35.201: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:35.201: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:35.218: 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: 19:04:35.218: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:35.218: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:35.234: 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: 19:04:35.234: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 19:04:35.237: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:38.206: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:42.625: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:42.625: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:42.642: 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: 19:04:42.642: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:42.642: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:04:42.660: 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: 19:04:42.661: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 19:04:43.343: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 19:04:44.021: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 19:04:44.021: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 19:04:44.039: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 19:04:44.039: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 19:04:44.039: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 19:04:44.057: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 19:04:44.057: Processing model [a:o] ** Message: 19:04:44.058: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 19:04:44.058: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 19:04:44.059: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 19:04:45.369: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 19:04:47.193: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 19:04:49.278: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:04:50.979: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:04:52.829: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 19:04:52.829: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 19:04:52.846: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 19:04:52.846: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 19:04:52.846: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 19:04:52.863: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 19:04:52.863: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 19:04:52.864: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 19:04:52.881: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 19:04:52.881: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:04:52.881: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:04:52.898: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 19:04:52.899: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:04:52.899: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:04:52.916: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:04:52.916: Processing model [e2g] ** Message: 19:04:52.917: Bootstrapper processing model [est2genome] ** Message: 19:04:52.917: Process optimal [optimal:est2genome] ** Message: 19:04:52.920: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c ** Message: 19:04:55.509: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c ** Message: 19:04:59.274: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c ** Message: 19:05:02.865: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 19:05:12.484: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 19:05:24.905: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 19:05:24.905: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o ** Message: 19:05:24.925: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 19:05:24.925: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 19:05:24.925: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o ** Message: 19:05:24.950: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 19:05:24.950: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 19:05:24.950: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o ** Message: 19:05:24.970: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 19:05:24.970: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 19:05:24.971: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 19:05:24.991: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 19:05:24.991: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 19:05:24.991: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 19:05:25.013: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 19:05:25.030: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 19:05:25.033: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:29.066: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:34.774: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:34.774: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:34.796: 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: 19:05:34.796: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:34.796: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:34.818: 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: 19:05:34.818: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 19:05:34.826: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:37.292: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:40.799: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:40.799: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:40.820: 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: 19:05:40.820: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:40.820: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:40.841: 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: 19:05:40.842: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 19:05:40.845: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:44.517: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:49.867: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:49.867: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:49.889: 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: 19:05:49.889: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:49.889: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:49.911: 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: 19:05:49.911: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 19:05:49.913: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:52.071: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:55.083: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:55.083: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:55.107: 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: 19:05:55.107: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:55.107: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:05:55.129: 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: 19:05:55.129: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 19:05:55.135: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:02.334: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:13.554: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:13.554: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:13.576: 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: 19:06:13.576: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:13.576: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:13.600: 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: 19:06:13.600: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 19:06:13.602: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:15.756: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:18.902: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:18.902: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:18.928: 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: 19:06:18.928: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:18.928: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:18.951: 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: 19:06:18.951: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 19:06:18.957: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:28.299: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:28.299: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:28.323: 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: 19:06:28.323: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 19:06:28.327: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:32.232: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:38.304: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:38.304: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:38.328: 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: 19:06:38.328: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:38.328: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:38.353: 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: 19:06:38.353: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 19:06:38.359: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:46.029: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:57.721: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:57.722: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:57.747: 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: 19:06:57.748: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:57.748: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:06:57.775: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 19:06:57.775: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 19:06:57.778: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:00.135: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:03.445: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:03.445: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:03.472: 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: 19:07:03.472: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:03.472: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:03.502: 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: 19:07:03.502: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 19:07:03.508: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:13.347: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:13.347: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:13.381: 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: 19:07:13.381: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 19:07:13.384: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:17.671: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:23.954: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:23.954: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:23.984: 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: 19:07:23.984: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:23.984: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:24.013: 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: 19:07:24.015: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:07:25.378: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:07:26.818: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:07:26.818: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:07:26.847: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:07:26.847: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:07:26.847: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:07:26.875: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 19:07:26.875: Processing model [ner] ** Message: 19:07:26.876: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 19:07:26.876: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 19:07:26.876: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 19:07:27.722: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 19:07:28.767: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 19:07:29.853: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:07:31.936: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:07:34.454: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 19:07:34.454: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 19:07:34.485: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 19:07:34.485: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 19:07:34.485: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 19:07:34.514: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 19:07:34.514: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 19:07:34.514: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 19:07:34.545: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 19:07:34.545: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:07:34.545: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:07:34.577: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 19:07:34.577: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:07:34.577: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:07:34.609: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:07:34.618: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:07:34.620: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:36.457: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:39.214: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:07:39.214: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:07:39.244: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 19:07:39.244: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:07:39.244: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:07:39.276: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:07:39.277: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 19:07:39.278: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:40.735: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:42.757: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:07:42.757: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:07:42.790: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 19:07:42.790: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:07:42.791: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:07:42.824: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:07:42.824: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:07:42.828: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:47.043: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:55.354: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:07:55.354: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:07:55.390: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 19:07:55.390: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:07:55.390: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:07:55.428: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:07:55.428: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 19:07:55.430: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:07:57.402: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:00.038: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:08:00.038: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:08:00.075: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 19:08:00.075: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:08:00.075: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:08:00.112: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:08:00.112: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 19:08:00.120: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:07.648: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:08:07.648: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:08:07.689: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:08:07.689: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:08:07.691: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:10.284: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:14.249: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:08:14.249: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:08:14.288: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 19:08:14.288: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:08:14.288: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:08:14.331: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:08:14.333: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 19:08:15.261: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 19:08:16.297: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:08:16.297: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 19:08:16.336: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 19:08:16.336: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 19:08:16.336: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 19:08:16.379: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 19:08:16.380: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 19:08:16.380: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 19:08:16.381: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 19:08:17.287: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 19:08:18.541: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 19:08:19.850: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:08:22.310: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:08:25.192: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 19:08:25.192: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 19:08:25.232: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 19:08:25.232: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 19:08:25.232: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 19:08:25.271: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 19:08:25.271: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 19:08:25.271: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 19:08:25.312: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 19:08:25.313: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:08:25.313: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:08:25.354: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 19:08:25.355: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:08:25.355: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:08:25.408: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:08:25.417: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:08:25.420: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:27.516: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:30.643: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:08:30.643: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:08:30.689: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 19:08:30.689: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:08:30.689: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:08:30.728: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:08:30.729: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 19:08:30.730: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:32.390: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:34.656: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:08:34.656: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:08:34.698: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 19:08:34.698: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:08:34.698: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:08:34.736: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:08:34.737: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:08:34.741: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:39.893: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:47.872: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:08:47.872: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:08:47.916: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 19:08:47.916: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:08:47.916: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:08:47.964: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:08:47.965: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 19:08:47.966: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:49.947: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:52.398: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:08:52.398: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:08:52.444: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 19:08:52.444: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:08:52.444: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:08:52.489: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:08:52.489: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 19:08:52.494: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:08:59.684: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:08:59.684: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:08:59.728: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:08:59.728: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:08:59.731: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:02.276: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:06.222: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:09:06.222: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:09:06.263: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 19:09:06.264: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:09:06.264: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:09:06.314: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 19:09:06.315: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 19:09:07.254: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 19:09:08.298: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:09:08.298: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 19:09:08.339: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 19:09:08.339: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 19:09:08.339: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 19:09:08.383: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 19:09:08.383: Processing model [p2d] ** Message: 19:09:08.384: Bootstrapper processing model [protein2dna:local] ** Message: 19:09:08.384: Process optimal [optimal:protein2dna:local] ** Message: 19:09:08.386: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 19:09:09.996: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 19:09:12.097: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 19:09:14.378: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 19:09:19.893: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 19:09:25.661: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 19:09:25.661: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 19:09:25.709: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 19:09:25.709: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 19:09:25.709: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 19:09:25.755: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 19:09:25.755: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 19:09:25.755: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 19:09:25.802: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 19:09:25.802: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 19:09:25.802: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 19:09:25.849: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 19:09:25.849: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 19:09:25.849: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 19:09:25.897: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 19:09:25.914: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 19:09:25.919: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:30.105: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:36.363: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:09:36.363: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:09:36.409: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 19:09:36.409: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:09:36.409: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:09:36.455: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 19:09:36.455: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 19:09:36.458: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:38.955: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:42.558: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:09:42.558: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:09:42.604: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 19:09:42.604: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:09:42.604: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:09:42.651: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 19:09:42.651: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 19:09:42.661: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:09:50.965: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:10:03.762: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:10:03.762: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:10:03.811: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 19:10:03.811: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:10:03.811: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:10:03.859: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 19:10:03.860: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 19:10:04.934: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 19:10:06.076: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 19:10:06.076: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 19:10:06.128: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 19:10:06.128: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 19:10:06.128: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 19:10:06.178: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 19:10:06.178: Processing model [p2d:b] ** Message: 19:10:06.179: Bootstrapper processing model [protein2dna:bestfit] ** Message: 19:10:06.179: Process optimal [optimal:protein2dna:bestfit] ** Message: 19:10:06.184: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 19:10:11.232: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 19:10:18.426: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 19:10:25.311: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 19:10:30.588: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 19:10:36.213: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 19:10:36.213: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 19:10:36.259: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 19:10:36.259: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 19:10:36.259: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 19:10:36.359: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 19:10:36.359: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 19:10:36.359: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 19:10:36.456: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 19:10:36.456: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 19:10:36.456: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 19:10:36.512: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 19:10:36.512: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 19:10:36.512: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 19:10:36.574: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 19:10:36.574: Processing model [p2g] ** Message: 19:10:36.576: Bootstrapper processing model [protein2genome:local] ** Message: 19:10:36.576: Process optimal [optimal:protein2genome:local] ** Message: 19:10:36.579: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 19:10:41.075: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 19:10:47.455: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 19:10:52.973: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 19:11:11.913: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 19:11:34.996: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 19:11:34.996: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 19:11:35.046: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 19:11:35.046: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 19:11:35.046: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 19:11:35.097: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 19:11:35.097: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 19:11:35.097: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 19:11:35.148: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 19:11:35.148: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 19:11:35.148: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 19:11:35.198: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 19:11:35.198: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 19:11:35.198: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 19:11:35.249: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 19:11:35.316: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 19:11:35.326: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:11:51.438: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:12:19.196: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:12:19.196: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:12:19.249: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:12:19.249: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:12:19.249: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:12:19.303: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:12:19.303: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 19:12:19.308: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:12:28.189: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:12:41.587: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:12:41.587: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:12:41.646: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:12:41.646: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:12:41.646: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:12:41.703: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:12:41.703: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 19:12:41.720: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:13:22.133: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:14:38.156: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:14:38.156: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:14:38.213: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:14:38.214: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:14:38.214: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:14:38.272: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:14:38.272: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 19:14:38.278: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:14:47.227: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:15:01.068: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:15:01.068: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:15:01.125: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:15:01.125: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:15:01.125: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:15:01.182: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:15:01.182: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 19:15:01.199: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:16:00.548: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:16:00.548: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:16:00.617: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:16:00.618: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:16:00.628: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:16:19.338: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:16:51.464: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:16:51.464: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:16:51.527: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:16:51.527: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:16:51.527: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:16:51.592: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:16:51.592: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 19:16:51.598: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:17:00.737: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:17:14.908: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:17:14.908: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:17:14.971: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:17:14.971: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:17:14.971: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:17:15.033: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:17:15.033: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 19:17:15.053: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:18:15.171: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:18:15.171: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:18:15.248: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:18:15.248: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:18:15.258: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:18:35.447: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:19:09.047: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:19:09.048: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:19:09.110: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:19:09.110: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:19:09.110: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:19:09.176: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:19:09.176: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 19:19:09.182: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:19:18.082: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:19:31.798: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:19:31.799: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:19:31.866: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:19:31.867: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:19:31.867: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:19:31.934: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:19:31.934: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 19:19:31.951: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:20:31.113: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:20:31.114: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:20:31.185: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:20:31.185: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:20:31.195: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:20:49.326: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:21:21.215: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:21:21.215: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:21:21.297: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 19:21:21.297: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:21:21.297: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:21:21.370: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 19:21:21.373: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 19:21:23.095: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 19:21:25.060: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:21:25.060: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 19:21:25.144: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 19:21:25.144: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 19:21:25.144: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 19:21:25.220: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 19:21:25.221: Processing model [p2g:b] ** Message: 19:21:25.222: Bootstrapper processing model [protein2genome:bestfit] ** Message: 19:21:25.222: Process optimal [optimal:protein2genome:bestfit] ** Message: 19:21:25.234: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 19:21:46.739: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 19:22:26.386: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 19:22:53.709: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 19:23:13.463: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 19:23:37.867: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 19:23:37.867: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 19:23:37.939: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 19:23:37.940: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 19:23:37.940: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 19:23:38.013: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 19:23:38.013: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 19:23:38.013: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 19:23:38.087: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 19:23:38.087: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 19:23:38.087: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 19:23:38.179: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 19:23:38.179: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 19:23:38.179: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 19:23:38.263: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 19:23:38.263: Processing model [c2c] ** Message: 19:23:38.265: Bootstrapper processing model [coding2coding] ** Message: 19:23:38.265: Process optimal [optimal:coding2coding] ** Message: 19:23:38.269: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c ** Message: 19:23:41.976: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c ** Message: 19:23:47.436: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c ** Message: 19:23:53.709: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 19:24:09.938: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 19:24:27.733: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 19:24:27.733: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o ** Message: 19:24:27.816: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 19:24:27.816: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 19:24:27.816: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o ** Message: 19:24:27.898: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 19:24:27.898: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 19:24:27.898: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o ** Message: 19:24:27.985: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 19:24:27.985: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 19:24:27.985: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 19:24:28.062: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 19:24:28.062: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 19:24:28.062: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 19:24:28.141: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 19:24:28.228: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 19:24:28.241: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:24:40.750: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:25:01.422: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:25:01.422: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:25:01.505: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 19:25:01.505: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:25:01.505: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:25:01.585: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 19:25:01.585: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 19:25:01.590: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:25:07.530: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:25:16.233: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:25:16.233: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:25:16.314: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 19:25:16.314: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:25:16.315: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:25:16.399: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 19:25:16.399: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 19:25:16.413: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:25:41.323: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_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: 19:26:23.580: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:26:23.580: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:26:23.657: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 19:26:23.657: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:26:23.657: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:26:23.736: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 19:26:23.738: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 19:26:24.955: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 19:26:26.297: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 19:26:26.297: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 19:26:26.381: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 19:26:26.381: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 19:26:26.381: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 19:26:26.464: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 19:26:26.464: Processing model [c2g] ** Message: 19:26:26.466: Bootstrapper processing model [coding2genome] ** Message: 19:26:26.466: Process optimal [optimal:coding2genome] ** Message: 19:26:26.474: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c ** Message: 19:26:38.577: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c ** Message: 19:26:57.035: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c ** Message: 19:27:13.784: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 19:28:20.993: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 19:30:03.270: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 19:30:03.270: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o ** Message: 19:30:03.360: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 19:30:03.360: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 19:30:03.360: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o ** Message: 19:30:03.474: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 19:30:03.474: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 19:30:03.474: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o ** Message: 19:30:03.579: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 19:30:03.579: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 19:30:03.579: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 19:30:03.669: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 19:30:03.669: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 19:30:03.669: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 19:30:03.757: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 19:30:03.759: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:30:05.734: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:30:08.041: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:30:08.041: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:30:08.146: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:30:08.146: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:30:08.146: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:30:08.267: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 19:30:08.268: Processing model [cd2g] ** Message: 19:30:08.271: Bootstrapper processing model [cdna2genome] ** Message: 19:30:08.271: Process optimal [optimal:cdna2genome] ** Message: 19:30:08.284: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c ** Message: 19:30:44.064: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c ** Message: 19:31:45.639: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c ** Message: 19:32:40.726: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 19:36:10.185: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 19:41:49.548: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 19:41:49.548: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o ** Message: 19:41:49.630: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 19:41:49.630: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 19:41:49.630: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o ** Message: 19:41:49.714: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 19:41:49.714: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 19:41:49.714: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o ** Message: 19:41:49.806: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 19:41:49.806: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 19:41:49.806: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 19:41:49.897: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 19:41:49.897: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 19:41:49.897: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 19:41:49.984: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 19:41:49.987: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:41:52.883: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:41:56.323: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:41:56.323: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:41:56.421: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:41:56.421: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:41:56.421: Adding object file [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:41:56.510: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 19:41:56.511: Compiling with: [gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/sequence -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 19:41:57.473: Adding: [c4_model_lookup.o] ** Message: 19:41:57.473: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 19:41:57.561: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 19:41:57.735: Done ** Message: 19:41:57.735: Finished building bootstrapping components make all-am make[4]: Entering directory '/build/exonerate-2.4.0/src/program' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate.o exonerate.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/sdp/scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ipcress.o ipcress.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate-server.o exonerate-server.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:84, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:212:23: note: declared here 212 | 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:212:23: note: declared here 212 | gchar* g_strup (gchar *string); | ^~~~~~~ exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 354 | g_string_sprintfa(str, " %d %d %d", | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 357 | g_string_sprintfa(str, "\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c: In function 'Exonerate_Server_process': exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] 669 | (*reply) = g_strdup_printf("dbinfo: %s %s" | ^~~~~~~~~~~~~~~ ...... 676 | server->dataset->header->number_of_seqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | guint64 {aka long unsigned int} exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] 669 | (*reply) = g_strdup_printf("dbinfo: %s %s" | ^~~~~~~~~~~~~~~ ...... 677 | server->dataset->header->max_seq_len, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | guint64 {aka long unsigned int} exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'guint64' {aka 'long unsigned int'} [-Wformat=] 669 | (*reply) = g_strdup_printf("dbinfo: %s %s" | ^~~~~~~~~~~~~~~ ...... 678 | server->dataset->header->total_seq_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | guint64 {aka long unsigned int} gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 make[4]: Leaving directory '/build/exonerate-2.4.0/src/program' make[3]: Leaving directory '/build/exonerate-2.4.0/src/program' Making all in util make[3]: Entering directory '/build/exonerate-2.4.0/src/util' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaclean.o fastaclean.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaclip.o fastaclip.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastachecksum.o fastachecksum.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastacomposition.o fastacomposition.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastadiff.o fastadiff.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaexplode.o fastaexplode.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastafetch.o fastafetch.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastahardmask.o fastahardmask.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; | ^~~~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaindex.o fastaindex.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastalength.o fastalength.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastanrdb.o fastanrdb.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaoverlap.o fastaoverlap.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(query, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastareformat.o fastareformat.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaremove.o fastaremove.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastarevcomp.o fastarevcomp.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasoftmask.o fastasoftmask.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasort.o fastasort.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasplit.o fastasplit.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasubseq.o fastasubseq.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastatranslate.o fastatranslate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastavalidcds.o fastavalidcds.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fasta2esd.o fasta2esd.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaannotatecdna.o fastaannotatecdna.c 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); | ^~~~~~~~~~ fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib.h:84, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | 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:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o esd2esi.o esd2esi.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_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/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/exonerate-2.4.0/src' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/src' make[2]: Leaving directory '/build/exonerate-2.4.0/src' Making all in test make[2]: Entering directory '/build/exonerate-2.4.0/test' Making all in data make[3]: Entering directory '/build/exonerate-2.4.0/test/data' Making all in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making all in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making all in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making all in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making all in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Entering directory '/build/exonerate-2.4.0' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/exonerate-2.4.0' make[1]: Leaving directory '/build/exonerate-2.4.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/exonerate-2.4.0' /usr/bin/make -C test check make[2]: Entering directory '/build/exonerate-2.4.0/test' Making check in data make[3]: Entering directory '/build/exonerate-2.4.0/test/data' Making check in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making check in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making check in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[5]: Entering directory '/build/exonerate-2.4.0/test/exonerate' PASS: exonerate.simple.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making check in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[5]: Entering directory '/build/exonerate-2.4.0/test/ipcress' PASS: ipcress.simple.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making check in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' /usr/bin/make check-TESTS make[4]: Entering directory '/build/exonerate-2.4.0/test/util' make[5]: Entering directory '/build/exonerate-2.4.0/test/util' PASS: fastaclean.test.sh PASS: fastaclip.test.sh PASS: fastacomposition.test.sh PASS: fastadiff.test.sh PASS: fastaexpode.test.sh PASS: fastaindex.fastafetch.test.sh PASS: fastalength.test.sh PASS: fastanrdb.test.sh PASS: fastaoverlap.test.sh PASS: fastarefomat.test.sh PASS: fastaremove.test.sh PASS: fastarevcomp.test.sh PASS: fastasoftmask.fastahardmask.test.sh PASS: fastasort.test.sh PASS: fastasplit.test.sh PASS: fastasubseq.test.sh PASS: fastatranslate.test.sh PASS: fastavalidcds.test.sh ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 18 # PASS: 18 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/exonerate-2.4.0/test/util' make[4]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[1]: Leaving directory '/build/exonerate-2.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/exonerate/ make -j8 install DESTDIR=/build/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/exonerate-2.4.0' Making install in doc make[2]: Entering directory '/build/exonerate-2.4.0/doc' Making install in man make[3]: Entering directory '/build/exonerate-2.4.0/doc/man' Making install in man1 make[4]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[5]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' /usr/bin/install -c -m 644 exonerate.1 ipcress.1 exonerate-server.1 fastautils.1 '/build/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' make[5]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/build/exonerate-2.4.0/doc/man' make[5]: Entering directory '/build/exonerate-2.4.0/doc/man' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/build/exonerate-2.4.0/doc/man' make[3]: Entering directory '/build/exonerate-2.4.0/doc' make[4]: Entering directory '/build/exonerate-2.4.0/doc' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/doc' make[3]: Leaving directory '/build/exonerate-2.4.0/doc' make[2]: Leaving directory '/build/exonerate-2.4.0/doc' Making install in src make[2]: Entering directory '/build/exonerate-2.4.0/src' Making install in struct make[3]: Entering directory '/build/exonerate-2.4.0/src/struct' make[4]: Entering directory '/build/exonerate-2.4.0/src/struct' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/struct' make[3]: Leaving directory '/build/exonerate-2.4.0/src/struct' Making install in general make[3]: Entering directory '/build/exonerate-2.4.0/src/general' make[4]: Entering directory '/build/exonerate-2.4.0/src/general' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/general' make[3]: Leaving directory '/build/exonerate-2.4.0/src/general' Making install in sequence make[3]: Entering directory '/build/exonerate-2.4.0/src/sequence' make[4]: Entering directory '/build/exonerate-2.4.0/src/sequence' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/sequence' make[3]: Leaving directory '/build/exonerate-2.4.0/src/sequence' Making install in comparison make[3]: Entering directory '/build/exonerate-2.4.0/src/comparison' make[4]: Entering directory '/build/exonerate-2.4.0/src/comparison' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/comparison' make[3]: Leaving directory '/build/exonerate-2.4.0/src/comparison' Making install in database make[3]: Entering directory '/build/exonerate-2.4.0/src/database' make[4]: Entering directory '/build/exonerate-2.4.0/src/database' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/database' make[3]: Leaving directory '/build/exonerate-2.4.0/src/database' Making install in c4 make[3]: Entering directory '/build/exonerate-2.4.0/src/c4' make[4]: Entering directory '/build/exonerate-2.4.0/src/c4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/c4' make[3]: Leaving directory '/build/exonerate-2.4.0/src/c4' Making install in bsdp make[3]: Entering directory '/build/exonerate-2.4.0/src/bsdp' make[4]: Entering directory '/build/exonerate-2.4.0/src/bsdp' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' make[3]: Leaving directory '/build/exonerate-2.4.0/src/bsdp' Making install in sdp make[3]: Entering directory '/build/exonerate-2.4.0/src/sdp' make[4]: Entering directory '/build/exonerate-2.4.0/src/sdp' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/sdp' make[3]: Leaving directory '/build/exonerate-2.4.0/src/sdp' Making install in model make[3]: Entering directory '/build/exonerate-2.4.0/src/model' make[4]: Entering directory '/build/exonerate-2.4.0/src/model' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/model' make[3]: Leaving directory '/build/exonerate-2.4.0/src/model' Making install in hub make[3]: Entering directory '/build/exonerate-2.4.0/src/hub' make[4]: Entering directory '/build/exonerate-2.4.0/src/hub' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src/hub' make[3]: Leaving directory '/build/exonerate-2.4.0/src/hub' Making install in program make[3]: Entering directory '/build/exonerate-2.4.0/src/program' make install-am make[4]: Entering directory '/build/exonerate-2.4.0/src/program' make[5]: Entering directory '/build/exonerate-2.4.0/src/program' make[5]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' /usr/bin/install -c exonerate ipcress exonerate-server '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[5]: Leaving directory '/build/exonerate-2.4.0/src/program' make[4]: Leaving directory '/build/exonerate-2.4.0/src/program' make[3]: Leaving directory '/build/exonerate-2.4.0/src/program' Making install in util make[3]: Entering directory '/build/exonerate-2.4.0/src/util' make[4]: Entering directory '/build/exonerate-2.4.0/src/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' /usr/bin/install -c fastaclean fastaclip fastachecksum fastacomposition fastadiff fastaexplode fastafetch fastahardmask fastaindex fastalength fastanrdb fastaoverlap fastareformat fastaremove fastarevcomp fastasoftmask fastasort fastasplit fastasubseq fastatranslate fastavalidcds fasta2esd fastaannotatecdna esd2esi '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[4]: Leaving directory '/build/exonerate-2.4.0/src/util' make[3]: Leaving directory '/build/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/exonerate-2.4.0/src' make[4]: Entering directory '/build/exonerate-2.4.0/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/src' make[3]: Leaving directory '/build/exonerate-2.4.0/src' make[2]: Leaving directory '/build/exonerate-2.4.0/src' Making install in test make[2]: Entering directory '/build/exonerate-2.4.0/test' Making install in data make[3]: Entering directory '/build/exonerate-2.4.0/test/data' Making install in cdna make[4]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[5]: Entering directory '/build/exonerate-2.4.0/test/data/cdna' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/cdna' Making install in protein make[4]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[5]: Entering directory '/build/exonerate-2.4.0/test/data/protein' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/build/exonerate-2.4.0/test/data' make[5]: Entering directory '/build/exonerate-2.4.0/test/data' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/exonerate-2.4.0/test/data' make[4]: Leaving directory '/build/exonerate-2.4.0/test/data' make[3]: Leaving directory '/build/exonerate-2.4.0/test/data' Making install in exonerate make[3]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Entering directory '/build/exonerate-2.4.0/test/exonerate' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' make[3]: Leaving directory '/build/exonerate-2.4.0/test/exonerate' Making install in ipcress make[3]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Entering directory '/build/exonerate-2.4.0/test/ipcress' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' make[3]: Leaving directory '/build/exonerate-2.4.0/test/ipcress' Making install in util make[3]: Entering directory '/build/exonerate-2.4.0/test/util' make[4]: Entering directory '/build/exonerate-2.4.0/test/util' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Leaving directory '/build/exonerate-2.4.0/test/util' make[3]: Entering directory '/build/exonerate-2.4.0/test' make[4]: Entering directory '/build/exonerate-2.4.0/test' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/exonerate-2.4.0/test' make[3]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Leaving directory '/build/exonerate-2.4.0/test' make[2]: Entering directory '/build/exonerate-2.4.0' make[3]: Entering directory '/build/exonerate-2.4.0' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/exonerate-2.4.0' make[2]: Leaving directory '/build/exonerate-2.4.0' make[1]: Leaving directory '/build/exonerate-2.4.0' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/exonerate-2.4.0' dh_installchangelogs -k ChangeLog make[1]: Leaving directory '/build/exonerate-2.4.0' debian/rules override_dh_installexamples make[1]: Entering directory '/build/exonerate-2.4.0' dh_installexamples mkdir -p /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples; cp -a test/* /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples/; find /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples \( -name "Makefile*" -o -name "*.log" -o -name "*.trs" \) -exec rm \{\} \; for testfile in `find /build/exonerate-2.4.0/debian/exonerate/usr/share/doc/exonerate/examples -name "*.sh"` ; do \ sed -i -e "s#../../src/util/#/usr/bin/#" \ -e "s#../../src/program/#/usr/bin/#" \ -e "s#../data/#./data/#" \ ${testfile} ; \ done make[1]: Leaving directory '/build/exonerate-2.4.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'exonerate' in '../exonerate_2.4.0-5_arm64.deb'. dpkg-deb: building package 'exonerate-dbgsym' in '../exonerate-dbgsym_2.4.0-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../exonerate_2.4.0-5_arm64.buildinfo dpkg-genchanges --build=binary -O../exonerate_2.4.0-5_arm64.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/16674 and its subdirectories I: Current time: Sun May 7 19:42:28 -12 2023 I: pbuilder-time-stamp: 1683531748 Mon May 8 07:42:31 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net. Mon May 8 07:42:31 UTC 2023 I: Preparing to do remote build '2' on codethink13-arm64.debian.net. Mon May 8 08:26:52 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. Mon May 8 08:26:53 UTC 2023 I: exonerate_2.4.0-5_arm64.changes: Format: 1.8 Date: Thu, 03 Dec 2020 21:56:27 +0100 Source: exonerate Binary: exonerate exonerate-dbgsym Architecture: arm64 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: cf7a97f28a30261370bebd7856783b94cbd1df04 5723172 exonerate-dbgsym_2.4.0-5_arm64.deb 5efc102e1e37094558806dae80ee03f62f1ef841 6289 exonerate_2.4.0-5_arm64.buildinfo 664adc545047d592e4dc0ab83060bbe30fbe84fd 1480400 exonerate_2.4.0-5_arm64.deb Checksums-Sha256: 8313e48eb6f34baf34c871acddc481c0768722c3729c21f9e57e9adc26fb7ec4 5723172 exonerate-dbgsym_2.4.0-5_arm64.deb 620ea6f5dcc3cd31ed2865a5cc6ec7601c8a8a9466d15b4840498c9074b1bc95 6289 exonerate_2.4.0-5_arm64.buildinfo 3adef5a155d3f72180dc75225a070a2f07c7a973a1a0cfb05f1f10ef0ebb712e 1480400 exonerate_2.4.0-5_arm64.deb Files: b95f4565729c23127e752dcbeb0dc356 5723172 debug optional exonerate-dbgsym_2.4.0-5_arm64.deb 0da936ebe209246d4382434bf5a380dd 6289 science optional exonerate_2.4.0-5_arm64.buildinfo 008dad5eb485f9239d4849c320fbd328 1480400 science optional exonerate_2.4.0-5_arm64.deb Mon May 8 08:26:54 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/exonerate_2.4.0-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/exonerate_2.4.0-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/exonerate_2.4.0-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/b1/exonerate_2.4.0-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8I43V6zo/b2/exonerate_2.4.0-5_arm64.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: 0.555s) 0.555s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.240s) 0.240s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon May 8 08:26:55 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Mon May 8 08:26:55 UTC 2023 I: exonerate from bookworm built successfully and reproducibly on arm64. Mon May 8 08:26:59 UTC 2023 I: Submitting .buildinfo files to external archives: Mon May 8 08:26:59 UTC 2023 I: Submitting 8.0K b1/exonerate_2.4.0-5_arm64.buildinfo.asc Mon May 8 08:27:00 UTC 2023 I: Submitting 8.0K b2/exonerate_2.4.0-5_arm64.buildinfo.asc Mon May 8 08:27:01 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 8 08:27:01 UTC 2023 I: Done submitting .buildinfo files. Mon May 8 08:27:01 UTC 2023 I: Removing signed exonerate_2.4.0-5_arm64.buildinfo.asc files: removed './b1/exonerate_2.4.0-5_arm64.buildinfo.asc' removed './b2/exonerate_2.4.0-5_arm64.buildinfo.asc'