I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 21 16:29:41 +14 2021 I: pbuilder-time-stamp: 1626834581 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [exonerate_2.4.0-5.dsc] I: copying [./exonerate_2.4.0.orig.tar.gz] I: copying [./exonerate_2.4.0-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.WZ1x4Cud/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 4 11:18:18 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./exonerate_2.4.0-5.dsc dpkg-source: info: extracting exonerate in exonerate-2.4.0 dpkg-source: info: unpacking exonerate_2.4.0.orig.tar.gz dpkg-source: info: unpacking exonerate_2.4.0-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build-as-needed.patch dpkg-source: info: applying manpages.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying manpagesyntax.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13580/tmp/hooks/D01_modify_environment starting debug: Running on codethink16-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/13580/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/13580/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=13580 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.JfqEYEMvco/pbuilderrc_WO1j --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JfqEYEMvco/b2 --logfile b2/build.log --extrapackages usrmerge exonerate_2.4.0-5.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 21 16:29 sh -> bash lrwxrwxrwx 1 root root 4 Jul 20 23:24 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/13580/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 ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however: Package libglib2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmount-dev{a} libmpdec3{a} libncurses-dev{a} libncurses6{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix2{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline-dev{a} libreadline8{a} libselinux1-dev{a} libsepol1-dev{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} uuid-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 129 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 uuid-dev arm64 2.36.1-7 [99.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libblkid-dev arm64 2.36.1-7 [228 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libffi-dev arm64 3.3-6 [53.2 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-data all 2.66.8-1 [1164 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-bin arm64 2.66.8-1 [137 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-dev-bin arm64 2.66.8-1 [177 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libsepol1-dev arm64 3.1-1 [329 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libpcre2-16-0 arm64 10.36-2 [202 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libpcre2-32-0 arm64 10.36-2 [193 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libpcre2-posix2 arm64 10.36-2 [49.0 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libpcre2-dev arm64 10.36-2 [645 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libselinux1-dev arm64 3.1-3 [171 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libmount-dev arm64 2.36.1-7 [77.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libpcre16-3 arm64 2:8.39-13 [236 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libpcre32-3 arm64 2:8.39-13 [229 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libpcrecpp0v5 arm64 2:8.39-13 [151 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libpcre3-dev arm64 2:8.39-13 [579 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-dev arm64 2.66.8-1 [1592 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libncurses-dev arm64 6.2+20201114-2 [335 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libreadline-dev arm64 8.1-1 [153 kB] Fetched 31.9 MB in 3s (12.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libsepol1-dev:arm64 (3.1-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libffi-dev:arm64 (3.3-6) ... Setting up libpcre2-16-0:arm64 (10.36-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libpcre2-32-0:arm64 (10.36-2) ... Setting up libglib2.0-data (2.66.8-1) ... Setting up uuid-dev:arm64 (2.36.1-7) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libpcre32-3:arm64 (2:8.39-13) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libpcre2-posix2:arm64 (10.36-2) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libblkid-dev:arm64 (2.36.1-7) ... Setting up libncurses-dev:arm64 (6.2+20201114-2) ... Setting up gettext (0.21-4) ... Setting up libpcre2-dev:arm64 (10.36-2) ... Setting up libtool (2.4.6-15) ... Setting up libselinux1-dev:arm64 (3.1-3) ... Setting up libpcre3-dev:arm64 (2:8.39-13) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libglib2.0-bin (2.66.8-1) ... Setting up m4 (1.4.18-5) ... Setting up libreadline-dev:arm64 (8.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libmount-dev:arm64 (2.36.1-7) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up libglib2.0-dev-bin (2.66.8-1) ... Setting up libglib2.0-dev:arm64 (2.66.8-1) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1127 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 23711 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/exonerate-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../exonerate_2.4.0-5_source.changes dpkg-buildpackage: info: source package exonerate dpkg-buildpackage: info: source version 2.4.0-5 dpkg-buildpackage: info: source distribution unstable 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 aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.in:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.in:9: installing './compile' src/bsdp/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/bsdp/Makefile.am: installing './depcomp' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' parallel-tests: installing './test-driver' src/c4/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/comparison/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/database/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/general/Makefile.am:9: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/hub/Makefile.am:5: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/model/Makefile.am:11: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/program/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/sdp/Makefile.am:7: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/sequence/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/struct/Makefile.am:14: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/util/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') make[1]: Leaving directory '/build/exonerate-2.4.0' dh_auto_configure ./configure --build=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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for strings.h... (cached) yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking build system type... 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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from rangetree.h:23, from rangetree.c:18: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 In file included from /usr/include/glib-2.0/glib.h:62, 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:334:32: note: in definition of macro 'g_message' 334 | __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:334:32: note: in definition of macro 'g_message' 334 | __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:334:32: note: in definition of macro 'g_message' 334 | __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:334:32: note: in definition of macro 'g_message' 334 | __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:334:32: note: in definition of macro 'g_message' 334 | __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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | fread(ba->data, sizeof(guchar), size, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitarray.c: In function 'BitArray_read_int': bitarray.c:189:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(&num, sizeof(guint64), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 140 | if(!g_strcasecmp(arg_string, false_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c: In function 'Argument_show_version': argument.c:173:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 173 | g_print("Built on %s\n", __DATE__); | ^~~~~~~~ argument.c: In function 'main': argument.c:306:13: warning: Deprecated pre-processor symbol 306 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 307 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:111, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here 261 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 502 | g_tree_traverse(arg->option_registry, Argument_set_env_var_func, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 559 | g_tree_traverse(arg->option_registry, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol, replace with 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol, replace with 169 | g_string_sprintfa(full_msg, "%s", msg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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:111, from jobqueue.h:23, from jobqueue.test.c:17: /usr/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here 261 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/general' Making all in sequence make[3]: Entering directory '/build/exonerate-2.4.0/src/sequence' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 317 | if(!g_strcasecmp(name, dna_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 320 | if(!g_strcasecmp(name, protein_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 323 | if(!g_strcasecmp(name, unknown_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 195 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 203 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 637 | g_strdown(query_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 638 | g_strdown(target_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 640 | g_strup(query_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 641 | g_strup(target_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 31 | pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 59 | register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 69 | g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 155 | register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 174 | g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | void g_mem_chunk_free (GMemChunk *mem_chunk, | ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 252 | g_strup(pcr_primer->forward); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 253 | g_strup(pcr_primer->revcomp); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 357 | pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 363 | pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 366 | pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", | ^~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 381 | g_mem_chunk_destroy(pcr->sensor_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 383 | g_mem_chunk_destroy(pcr->probe_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 384 | g_mem_chunk_destroy(pcr->match_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 268 | if(!g_strcasecmp(force_fsm, "none")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 273 | if(!g_strcasecmp(force_fsm, "normal")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 275 | if(!g_strcasecmp(force_fsm, "compact")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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:62, 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:334:32: note: in definition of macro 'g_message' 334 | __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:334:32: note: in definition of macro 'g_message' 334 | __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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 660 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 667 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 677 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 690 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 988 | g_strup(tg_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include\"" -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 124 | if(!g_strcasecmp(short_name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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:82, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here 88 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 329 | if(!g_strcasecmp(force_scan, "none")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 336 | } else if((!g_strcasecmp(force_scan, "query")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 337 | || (!g_strcasecmp(force_scan, "q"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 339 | } else if((!g_strcasecmp(force_scan, "target")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 340 | || (!g_strcasecmp(force_scan, "t"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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: 16:31:49.672: Starting building bootstrapping components ** Message: 16:31:49.672: Processing model [u] ** Message: 16:31:49.673: Bootstrapper processing model [ungapped:dna2dna] ** Message: 16:31:49.673: Process optimal [optimal:ungapped:dna2dna] ** (process:2107): WARNING **: 16:31:49.673: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:2107): WARNING **: 16:31:49.674: Creating codegen directory [/build/exonerate-2.4.0/codegen] ** (process:2107): WARNING **: 16:31:49.674: Creating codegen directory [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu] ** (process:2107): WARNING **: 16:31:49.674: Creating codegen directory [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu] ** Message: 16:31:49.674: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:50.210: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:50.724: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:51.289: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:52.153: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:53.016: 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: 16:31:53.016: 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: 16:31:53.022: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 16:31:53.022: 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: 16:31:53.022: 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: 16:31:53.027: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 16:31:53.027: 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: 16:31:53.027: 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: 16:31:53.032: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 16:31:53.033: 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: 16:31:53.033: 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: 16:31:53.038: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 16:31:53.038: 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: 16:31:53.038: 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: 16:31:53.043: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:31:53.044: Bootstrapper processing model [ungapped:protein2protein] ** Message: 16:31:53.044: Process optimal [optimal:ungapped:protein2protein] ** Message: 16:31:53.044: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:53.498: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:54.022: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:54.566: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:55.407: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:56.259: 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: 16:31:56.260: 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: 16:31:56.266: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 16:31:56.266: 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: 16:31:56.266: 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: 16:31:56.272: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 16:31:56.272: 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: 16:31:56.272: 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: 16:31:56.279: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 16:31:56.279: 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: 16:31:56.279: 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: 16:31:56.285: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 16:31:56.285: 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: 16:31:56.285: 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: 16:31:56.292: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:31:56.292: Bootstrapper processing model [ungapped:dna2protein] ** Message: 16:31:56.292: Process optimal [optimal:ungapped:dna2protein] ** Message: 16:31:56.293: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:56.859: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:57.553: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:58.412: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:31:59.425: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:00.604: 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: 16:32:00.604: 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: 16:32:00.610: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 16:32:00.611: 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: 16:32:00.611: 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: 16:32:00.617: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 16:32:00.617: 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: 16:32:00.617: 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: 16:32:00.624: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 16:32:00.624: 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: 16:32:00.624: 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: 16:32:00.630: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 16:32:00.631: 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: 16:32:00.631: 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: 16:32:00.639: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 16:32:00.640: Bootstrapper processing model [ungapped:protein2dna] ** Message: 16:32:00.640: Process optimal [optimal:ungapped:protein2dna] ** Message: 16:32:00.640: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:01.211: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:01.891: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:02.646: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:03.845: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:04.880: 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: 16:32:04.880: 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: 16:32:04.887: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 16:32:04.887: 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: 16:32:04.887: 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: 16:32:04.899: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 16:32:04.899: 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: 16:32:04.899: 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: 16:32:04.907: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 16:32:04.907: 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: 16:32:04.907: 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: 16:32:04.915: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 16:32:04.915: 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: 16:32:04.915: 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: 16:32:04.927: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 16:32:04.927: Processing model [u:t] ** Message: 16:32:04.927: Bootstrapper processing model [ungapped:codon] ** Message: 16:32:04.927: Process optimal [optimal:ungapped:codon] ** Message: 16:32:04.929: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:05.841: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:06.934: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:08.212: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:09.997: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:11.714: 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: 16:32:11.714: 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: 16:32:11.722: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 16:32:11.722: 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: 16:32:11.723: 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: 16:32:11.730: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 16:32:11.731: 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: 16:32:11.731: 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: 16:32:11.744: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 16:32:11.744: 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: 16:32:11.744: 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: 16:32:11.752: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 16:32:11.752: 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: 16:32:11.752: 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: 16:32:11.770: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 16:32:11.771: Processing model [a:g] ** Message: 16:32:11.771: Bootstrapper processing model [affine:global:dna2dna] ** Message: 16:32:11.771: Process optimal [optimal:affine:global:dna2dna] ** Message: 16:32:11.773: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:13.030: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:14.812: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:16.542: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:18.580: 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: 16:32:18.580: 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: 16:32:18.588: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 16:32:18.588: 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: 16:32:18.588: 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: 16:32:18.601: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 16:32:18.601: 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: 16:32:18.601: 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: 16:32:18.611: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 16:32:18.611: 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: 16:32:18.611: 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: 16:32:18.625: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:32:18.625: Bootstrapper processing model [affine:global:protein2protein] ** Message: 16:32:18.625: Process optimal [optimal:affine:global:protein2protein] ** Message: 16:32:18.627: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:19.799: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:21.482: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:23.155: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:25.206: 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: 16:32:25.206: 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: 16:32:25.216: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 16:32:25.216: 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: 16:32:25.216: 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: 16:32:25.226: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 16:32:25.226: 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: 16:32:25.226: 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: 16:32:25.236: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 16:32:25.236: 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: 16:32:25.236: 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: 16:32:25.246: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:32:25.246: Processing model [a:b] ** Message: 16:32:25.247: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 16:32:25.247: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 16:32:25.249: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:26.861: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:29.308: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:31.466: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:33.247: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:35.274: 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: 16:32:35.274: 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: 16:32:35.287: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 16:32:35.287: 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: 16:32:35.287: 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: 16:32:35.298: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 16:32:35.298: 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: 16:32:35.298: 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: 16:32:35.309: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 16:32:35.309: 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: 16:32:35.309: 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: 16:32:35.320: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 16:32:35.320: 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: 16:32:35.320: 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: 16:32:35.331: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:32:35.331: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 16:32:35.331: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 16:32:35.333: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:36.934: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:39.385: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:41.574: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:43.282: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:45.304: 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: 16:32:45.305: 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: 16:32:45.323: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 16:32:45.323: 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: 16:32:45.323: 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: 16:32:45.339: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 16:32:45.339: 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: 16:32:45.339: 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: 16:32:45.355: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 16:32:45.356: 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: 16:32:45.356: 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: 16:32:45.371: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 16:32:45.371: 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: 16:32:45.371: 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: 16:32:45.387: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:32:45.387: Processing model [a:l] ** Message: 16:32:45.387: Bootstrapper processing model [affine:local:dna2dna] ** Message: 16:32:45.387: Process optimal [optimal:affine:local:dna2dna] ** Message: 16:32:45.388: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:46.105: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:46.998: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:47.921: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:49.652: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:51.706: 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: 16:32:51.707: 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: 16:32:51.723: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:32:51.723: 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: 16:32:51.723: 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: 16:32:51.739: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:32:51.739: 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: 16:32:51.739: 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: 16:32:51.762: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:32:51.762: 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: 16:32:51.762: 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: 16:32:51.779: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:32:51.779: 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: 16:32:51.779: 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: 16:32:51.801: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:32:51.807: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 16:32:51.809: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:53.363: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:55.607: 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: 16:32:55.608: 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: 16:32:55.621: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:32:55.621: 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: 16:32:55.621: 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: 16:32:55.633: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:32:55.634: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 16:32:55.635: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:56.848: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:32:58.506: 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: 16:32:58.506: 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: 16:32:58.519: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:32:58.519: 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: 16:32:58.519: 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: 16:32:58.533: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:32:58.533: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 16:32:58.536: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:02.051: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:07.040: 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: 16:33:07.040: 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: 16:33:07.053: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:33:07.053: 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: 16:33:07.053: 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: 16:33:07.066: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:33:07.067: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:07.705: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:08.485: 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: 16:33:08.485: 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: 16:33:08.500: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 16:33:08.500: 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: 16:33:08.500: 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: 16:33:08.515: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 16:33:08.515: Bootstrapper processing model [affine:local:protein2protein] ** Message: 16:33:08.518: Process optimal [optimal:affine:local:protein2protein] ** Message: 16:33:08.519: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:09.155: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:10.332: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:11.257: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:12.954: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:14.946: 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: 16:33:14.946: 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: 16:33:14.960: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:33:14.960: 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: 16:33:14.960: 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: 16:33:14.975: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:33:14.975: 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: 16:33:14.975: 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: 16:33:14.989: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:33:14.989: 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: 16:33:14.989: 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: 16:33:15.004: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:33:15.004: 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: 16:33:15.004: 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: 16:33:15.018: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:33:15.022: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 16:33:15.024: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:16.422: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:18.478: 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: 16:33:18.479: 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: 16:33:18.493: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:33:18.493: 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: 16:33:18.493: 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: 16:33:18.507: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:33:18.507: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 16:33:18.508: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:19.633: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:21.229: 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: 16:33:21.229: 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: 16:33:21.244: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:33:21.244: 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: 16:33:21.244: 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: 16:33:21.259: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:33:21.259: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 16:33:21.263: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:24.527: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:29.410: 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: 16:33:29.411: 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: 16:33:29.428: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:33:29.428: 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: 16:33:29.428: 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: 16:33:29.443: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:33:29.447: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:30.124: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:30.789: 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: 16:33:30.789: 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: 16:33:30.805: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 16:33:30.805: 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: 16:33:30.805: 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: 16:33:30.820: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 16:33:30.821: Processing model [a:o] ** Message: 16:33:30.821: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 16:33:30.821: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 16:33:30.823: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:32.201: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:34.216: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:36.448: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:38.137: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:40.195: 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: 16:33:40.195: 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: 16:33:40.210: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 16:33:40.210: 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: 16:33:40.210: 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: 16:33:40.228: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 16:33:40.229: 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: 16:33:40.229: 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: 16:33:40.244: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 16:33:40.244: 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: 16:33:40.244: 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: 16:33:40.260: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 16:33:40.260: 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: 16:33:40.260: 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: 16:33:40.277: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:33:40.277: Processing model [e2g] ** Message: 16:33:40.278: Bootstrapper processing model [est2genome] ** Message: 16:33:40.278: Process optimal [optimal:est2genome] ** Message: 16:33:40.280: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:43.126: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:47.370: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:33:51.417: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:01.672: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:15.626: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 16:34:15.626: 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: 16:34:15.644: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 16:34:15.644: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 16:34:15.644: 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: 16:34:15.665: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 16:34:15.666: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 16:34:15.666: 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: 16:34:15.708: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 16:34:15.708: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 16:34:15.708: 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: 16:34:15.731: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 16:34:15.731: 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: 16:34:15.731: 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: 16:34:15.773: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 16:34:15.788: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 16:34:15.797: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:19.990: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:26.254: 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: 16:34:26.254: 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: 16:34:26.272: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:34:26.272: 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: 16:34:26.272: 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: 16:34:26.291: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:34:26.291: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 16:34:26.293: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:28.632: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:32.215: 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: 16:34:32.215: 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: 16:34:32.239: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:34:32.240: 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: 16:34:32.240: 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: 16:34:32.262: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:34:32.262: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 16:34:32.265: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:36.646: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:43.108: 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: 16:34:43.109: 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: 16:34:43.128: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:34:43.128: 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: 16:34:43.128: 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: 16:34:43.147: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:34:43.147: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 16:34:43.149: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:45.551: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:49.069: 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: 16:34:49.070: 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: 16:34:49.090: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:34:49.090: 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: 16:34:49.090: 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: 16:34:49.110: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:34:49.110: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 16:34:49.117: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:34:57.737: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:11.549: 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: 16:35:11.551: 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: 16:35:11.575: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:35:11.576: 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: 16:35:11.576: 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: 16:35:11.597: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:35:11.597: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:35:11.599: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:14.299: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:18.063: 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: 16:35:18.063: 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: 16:35:18.084: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:35:18.084: 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: 16:35:18.084: 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: 16:35:18.106: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:35:18.106: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:35:18.112: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:29.234: 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: 16:35:29.234: 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: 16:35:29.255: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:35:29.255: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 16:35:29.259: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:34.047: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:41.368: 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: 16:35:41.368: 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: 16:35:41.392: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:35:41.393: 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: 16:35:41.393: 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: 16:35:41.415: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:35:41.415: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 16:35:41.421: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:35:50.180: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:03.728: 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: 16:36:03.728: 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: 16:36:03.750: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:36:03.750: 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: 16:36:03.750: 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: 16:36:03.772: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:36:03.772: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:36:03.774: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:06.306: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:09.901: 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: 16:36:09.901: 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: 16:36:09.925: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:36:09.925: 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: 16:36:09.925: 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: 16:36:09.949: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:36:09.949: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:36:09.955: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:20.908: 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: 16:36:20.908: 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: 16:36:20.931: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:36:20.931: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 16:36:20.934: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:25.546: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:32.483: 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: 16:36:32.484: 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: 16:36:32.510: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:36:32.510: 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: 16:36:32.510: 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: 16:36:32.535: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:36:32.537: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:33.868: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:35.418: 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: 16:36:35.418: 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: 16:36:35.441: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:36:35.441: 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: 16:36:35.441: 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: 16:36:35.464: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 16:36:35.464: Processing model [ner] ** Message: 16:36:35.465: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 16:36:35.465: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 16:36:35.466: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:36.197: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:37.256: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:38.308: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:40.561: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:43.250: 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: 16:36:43.250: 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: 16:36:43.274: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:36:43.275: 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: 16:36:43.275: 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: 16:36:43.311: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:36:43.311: 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: 16:36:43.311: 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: 16:36:43.343: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:36:43.343: 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: 16:36:43.343: 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: 16:36:43.368: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:36:43.369: 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: 16:36:43.369: 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: 16:36:43.397: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:36:43.408: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:36:43.411: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:45.449: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:48.442: 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: 16:36:48.442: 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: 16:36:48.475: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:36:48.475: 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: 16:36:48.475: 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: 16:36:48.504: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:36:48.504: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 16:36:48.506: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:50.071: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:52.336: 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: 16:36:52.336: 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: 16:36:52.370: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:36:52.370: 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: 16:36:52.370: 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: 16:36:52.409: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:36:52.409: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:36:52.419: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:36:57.497: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:05.566: 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: 16:37:05.566: 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: 16:37:05.593: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:37:05.594: 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: 16:37:05.594: 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: 16:37:05.628: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:37:05.628: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:37:05.634: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:07.336: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:09.741: 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: 16:37:09.741: 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: 16:37:09.771: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:37:09.771: 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: 16:37:09.772: 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: 16:37:09.800: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:37:09.800: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:37:09.805: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:17.008: 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: 16:37:17.008: 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: 16:37:17.037: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:37:17.037: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:37:17.039: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:19.299: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:22.891: 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: 16:37:22.891: 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: 16:37:22.920: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:37:22.920: 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: 16:37:22.920: 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: 16:37:22.948: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:37:22.949: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:23.963: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:24.836: 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: 16:37:24.836: 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: 16:37:24.864: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 16:37:24.864: 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: 16:37:24.864: 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: 16:37:24.891: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 16:37:24.892: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 16:37:24.892: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 16:37:24.893: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:25.642: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:26.795: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:28.048: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:30.434: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:33.091: 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: 16:37:33.091: 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: 16:37:33.120: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:37:33.120: 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: 16:37:33.120: 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: 16:37:33.150: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:37:33.150: 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: 16:37:33.150: 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: 16:37:33.180: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:37:33.180: 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: 16:37:33.180: 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: 16:37:33.210: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:37:33.210: 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: 16:37:33.210: 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: 16:37:33.240: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:37:33.249: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:37:33.251: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:35.202: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:38.069: 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: 16:37:38.070: 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: 16:37:38.100: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:37:38.100: 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: 16:37:38.100: 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: 16:37:38.132: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:37:38.132: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 16:37:38.134: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:39.630: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:41.745: 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: 16:37:41.745: 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: 16:37:41.773: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:37:41.774: 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: 16:37:41.774: 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: 16:37:41.803: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:37:41.803: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:37:41.808: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:46.419: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:54.264: 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: 16:37:54.264: 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: 16:37:54.293: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:37:54.293: 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: 16:37:54.293: 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: 16:37:54.324: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:37:54.324: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:37:54.325: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:56.038: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:37:58.370: 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: 16:37:58.370: 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: 16:37:58.400: 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: 16:37:58.400: 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: 16:37:58.400: 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: 16:37:58.433: 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: 16:37:58.433: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:37:58.438: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:05.382: 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: 16:38:05.382: 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: 16:38:05.420: 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: 16:38:05.420: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:38:05.423: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:07.606: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:11.171: 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: 16:38:11.171: 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: 16:38:11.211: 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: 16:38:11.212: 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: 16:38:11.212: 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: 16:38:11.247: 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: 16:38:11.248: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:12.017: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:12.900: 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: 16:38:12.900: 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: 16:38:12.933: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 16:38:12.933: 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: 16:38:12.933: 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: 16:38:12.969: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 16:38:12.970: Processing model [p2d] ** Message: 16:38:12.970: Bootstrapper processing model [protein2dna:local] ** Message: 16:38:12.970: Process optimal [optimal:protein2dna:local] ** Message: 16:38:12.973: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:14.393: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:16.458: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:18.592: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:23.512: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:28.847: 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: 16:38:28.847: 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: 16:38:28.878: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 16:38:28.878: 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: 16:38:28.878: 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: 16:38:28.910: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 16:38:28.910: 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: 16:38:28.910: 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: 16:38:28.942: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 16:38:28.942: 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: 16:38:28.942: 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: 16:38:28.974: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 16:38:28.975: 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: 16:38:28.975: 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: 16:38:29.007: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 16:38:29.024: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 16:38:29.029: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:33.024: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:39.319: 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: 16:38:39.319: 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: 16:38:39.351: 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: 16:38:39.351: 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: 16:38:39.351: 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: 16:38:39.385: 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: 16:38:39.385: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 16:38:39.388: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:41.718: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:45.100: 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: 16:38:45.100: 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: 16:38:45.136: 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: 16:38:45.136: 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: 16:38:45.136: 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: 16:38:45.169: 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: 16:38:45.169: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 16:38:45.176: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:38:53.077: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:05.731: 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: 16:39:05.731: 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: 16:39:05.764: 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: 16:39:05.764: 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: 16:39:05.764: 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: 16:39:05.807: 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: 16:39:05.821: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:06.720: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:07.618: 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: 16:39:07.618: 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: 16:39:07.658: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 16:39:07.658: 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: 16:39:07.658: 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: 16:39:07.693: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 16:39:07.694: Processing model [p2d:b] ** Message: 16:39:07.694: Bootstrapper processing model [protein2dna:bestfit] ** Message: 16:39:07.694: Process optimal [optimal:protein2dna:bestfit] ** Message: 16:39:07.699: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:12.381: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:20.046: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:26.544: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:31.298: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:36.770: 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: 16:39:36.770: 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: 16:39:36.804: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 16:39:36.804: 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: 16:39:36.804: 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: 16:39:36.843: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 16:39:36.843: 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: 16:39:36.843: 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: 16:39:36.883: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 16:39:36.883: 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: 16:39:36.883: 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: 16:39:36.919: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 16:39:36.919: 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: 16:39:36.919: 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: 16:39:36.958: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 16:39:36.959: Processing model [p2g] ** Message: 16:39:36.960: Bootstrapper processing model [protein2genome:local] ** Message: 16:39:36.960: Process optimal [optimal:protein2genome:local] ** Message: 16:39:36.965: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:40.971: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:47.018: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:39:52.442: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:40:10.129: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:40:34.022: 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: 16:40:34.022: 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: 16:40:34.062: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 16:40:34.062: 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: 16:40:34.062: 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: 16:40:34.097: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 16:40:34.097: 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: 16:40:34.097: 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: 16:40:34.143: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 16:40:34.143: 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: 16:40:34.143: 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: 16:40:34.178: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 16:40:34.178: 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: 16:40:34.179: 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: 16:40:34.215: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 16:40:34.280: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 16:40:34.289: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:40:50.265: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:41:19.156: 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: 16:41:19.156: 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: 16:41:19.196: 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: 16:41:19.196: 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_path.o] ** Message: 16:41:19.196: 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_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: 16:41:19.238: 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: 16:41:19.238: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 16:41:19.249: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:41:27.396: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:41:40.199: 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: 16:41:40.199: 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: 16:41:40.245: 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: 16:41:40.245: 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: 16:41:40.245: 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: 16:41:40.286: 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: 16:41:40.286: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 16:41:40.310: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:42:17.289: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:43:33.364: 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: 16:43:33.364: 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: 16:43:33.407: 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: 16:43:33.407: 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: 16:43:33.407: 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: 16:43:33.448: 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: 16:43:33.449: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 16:43:33.454: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:43:41.641: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:43:54.411: 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: 16:43:54.411: 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: 16:43:54.452: 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: 16:43:54.452: 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: 16:43:54.452: 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: 16:43:54.494: 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: 16:43:54.494: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 16:43:54.510: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:44:53.448: 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: 16:44:53.448: 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: 16:44:53.492: 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: 16:44:53.492: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:44:53.502: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:45:10.210: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:45:41.161: 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: 16:45:41.161: 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: 16:45:41.204: 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: 16:45:41.204: 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: 16:45:41.204: 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: 16:45:41.247: 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: 16:45:41.248: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 16:45:41.253: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:45:49.604: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:46:02.478: 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: 16:46:02.478: 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: 16:46:02.538: 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: 16:46:02.538: 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: 16:46:02.538: 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: 16:46:02.590: 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: 16:46:02.590: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 16:46:02.607: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:47:00.399: 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: 16:47:00.399: 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: 16:47:00.446: 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: 16:47:00.446: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:47:00.456: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:47:17.469: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:47:49.130: 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: 16:47:49.130: 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: 16:47:49.180: 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: 16:47:49.180: 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: 16:47:49.180: 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: 16:47:49.231: 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: 16:47:49.231: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 16:47:49.237: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:47:58.236: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:48:12.048: 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: 16:48:12.048: 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: 16:48:12.098: 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: 16:48:12.098: 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: 16:48:12.098: 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: 16:48:12.145: 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: 16:48:12.145: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 16:48:12.168: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:49:12.409: 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: 16:49:12.410: 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: 16:49:12.465: 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: 16:49:12.465: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:49:12.476: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:49:29.682: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:50:01.174: 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: 16:50:01.174: 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: 16:50:01.226: 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: 16:50:01.226: 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: 16:50:01.226: 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: 16:50:01.282: 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: 16:50:01.285: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:50:02.725: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:50:04.515: 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: 16:50:04.515: 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: 16:50:04.566: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 16:50:04.566: 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: 16:50:04.566: 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: 16:50:04.617: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 16:50:04.618: Processing model [p2g:b] ** Message: 16:50:04.619: Bootstrapper processing model [protein2genome:bestfit] ** Message: 16:50:04.619: Process optimal [optimal:protein2genome:bestfit] ** Message: 16:50:04.631: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:50:25.639: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:51:02.541: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:51:27.300: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:51:45.014: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:07.884: 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: 16:52:07.884: 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: 16:52:07.933: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 16:52:07.933: 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: 16:52:07.933: 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: 16:52:07.982: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 16:52:07.982: 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: 16:52:07.982: 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: 16:52:08.032: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 16:52:08.032: 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: 16:52:08.032: 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: 16:52:08.083: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 16:52:08.083: 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: 16:52:08.083: 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: 16:52:08.134: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 16:52:08.134: Processing model [c2c] ** Message: 16:52:08.135: Bootstrapper processing model [coding2coding] ** Message: 16:52:08.135: Process optimal [optimal:coding2coding] ** Message: 16:52:08.139: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:11.513: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:16.964: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:22.659: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:36.856: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:52:53.992: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 16:52:53.992: 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: 16:52:54.056: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 16:52:54.057: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 16:52:54.057: 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: 16:52:54.113: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 16:52:54.113: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 16:52:54.113: 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: 16:52:54.188: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 16:52:54.188: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 16:52:54.188: 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: 16:52:54.298: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 16:52:54.298: 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: 16:52:54.298: 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: 16:52:54.400: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 16:52:54.478: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 16:52:54.490: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:53:06.254: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:53:27.523: 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: 16:53:27.523: 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: 16:53:27.590: 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: 16:53:27.590: 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: 16:53:27.590: 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: 16:53:27.649: 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: 16:53:27.649: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 16:53:27.654: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:53:32.972: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:53:41.436: 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: 16:53:41.436: 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: 16:53:41.527: 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: 16:53:41.527: 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: 16:53:41.527: 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: 16:53:41.599: 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: 16:53:41.599: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 16:53:41.613: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:54:07.315: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:54:50.689: 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: 16:54:50.689: 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: 16:54:50.767: 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: 16:54:50.767: 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: 16:54:50.767: 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: 16:54:50.833: 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: 16:54:50.834: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:54:51.979: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:54:53.151: 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: 16:54:53.154: 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: 16:54:53.214: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 16:54:53.214: 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: 16:54:53.214: 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: 16:54:53.286: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 16:54:53.287: Processing model [c2g] ** Message: 16:54:53.294: Bootstrapper processing model [coding2genome] ** Message: 16:54:53.294: Process optimal [optimal:coding2genome] ** Message: 16:54:53.305: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:55:04.175: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:55:22.532: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:55:38.124: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:56:41.479: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:58:21.897: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 16:58:21.897: 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: 16:58:21.954: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 16:58:21.954: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 16:58:21.954: 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: 16:58:22.012: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 16:58:22.012: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 16:58:22.012: 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: 16:58:22.071: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 16:58:22.071: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 16:58:22.071: 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: 16:58:22.130: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 16:58:22.130: 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: 16:58:22.130: 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: 16:58:22.190: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 16:58:22.191: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:58:23.891: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:58:26.005: 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: 16:58:26.005: 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: 16:58:26.074: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:58:26.074: 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: 16:58:26.074: 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: 16:58:26.140: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 16:58:26.141: Processing model [cd2g] ** Message: 16:58:26.147: Bootstrapper processing model [cdna2genome] ** Message: 16:58:26.147: Process optimal [optimal:cdna2genome] ** Message: 16:58:26.166: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:58:59.526: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 16:59:59.244: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:00:47.363: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:04:32.779: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:11:02.799: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 17:11:02.799: 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: 17:11:02.859: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 17:11:02.860: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 17:11:02.860: 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: 17:11:02.921: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 17:11:02.921: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 17:11:02.921: 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: 17:11:02.985: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 17:11:02.986: Adding: [/build/exonerate-2.4.0/codegen/aarch64_45_unknown_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 17:11:02.986: 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: 17:11:03.051: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 17:11:03.051: 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: 17:11:03.051: 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: 17:11:03.117: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 17:11:03.119: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:11:06.035: Compiling codegen: gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:11:09.566: 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: 17:11:09.566: 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: 17:11:09.635: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 17:11:09.635: 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: 17:11:09.635: 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: 17:11:09.705: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 17:11:09.706: Compiling with: [gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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: 17:11:10.739: Adding: [c4_model_lookup.o] ** Message: 17:11:10.740: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 17:11:10.812: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 17:11:10.953: Done ** Message: 17:11:10.953: Finished building bootstrapping components make all-am make[4]: Entering directory '/build/exonerate-2.4.0/src/program' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"aarch64-unknown-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol, replace with 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol, replace with 354 | g_string_sprintfa(str, " %d %d %d", | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol, replace with 357 | g_string_sprintfa(str, "\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=] 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=] ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 265 | g_strup(primer_b); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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:82, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(query, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 132 | else if(!g_strcasecmp(sort_key, "len")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 134 | else if(!g_strcasecmp(sort_key, "seq")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] 92 | output_dir, G_DIR_SEPARATOR, g_basename(query_path)); | ^~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/include/glib-2.0/glib/gfileutils.h:205:14: note: declared here 205 | const gchar *g_basename (const gchar *file_name); | ^~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 -fdebug-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/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 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' /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[5]: Nothing to be done for 'install-data-am'. /usr/bin/install -c exonerate ipcress exonerate-server '/build/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-dbgsym' in '../exonerate-dbgsym_2.4.0-5_arm64.deb'. dpkg-deb: building package 'exonerate' in '../exonerate_2.4.0-5_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../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: user script /srv/workspace/pbuilder/13580/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/13580/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/13580 and its subdirectories I: Current time: Wed Jul 21 17:11:55 +14 2021 I: pbuilder-time-stamp: 1626837115