I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 21 02:19:53 +14 2022 I: pbuilder-time-stamp: 1660997993 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [augustus_3.4.0+dfsg2-2.dsc] I: copying [./augustus_3.4.0+dfsg2.orig.tar.xz] I: copying [./augustus_3.4.0+dfsg2-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.GJIrrhcs/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 4 05:35:33 2021 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./augustus_3.4.0+dfsg2-2.dsc dpkg-source: info: extracting augustus in augustus-3.4.0+dfsg2 dpkg-source: info: unpacking augustus_3.4.0+dfsg2.orig.tar.xz dpkg-source: info: unpacking augustus_3.4.0+dfsg2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying interpreter_paths.patch dpkg-source: info: applying switch_cgp_testing_off.patch dpkg-source: info: applying disable-compare.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/45565/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. 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/45565/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/45565/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]="i686-pc-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=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=1176a1f7b5ea4093a581f1a385067278 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-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=45565 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.GRZu178kOl/pbuilderrc_aJAr --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.GRZu178kOl/b2 --logfile b2/build.log --extrapackages usrmerge augustus_3.4.0+dfsg2-2.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 2021 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 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 2021 more -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 21 02:20 sh -> bash lrwxrwxrwx 1 root root 4 Aug 20 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 2021 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/45565/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblpsolve55-dev; however: Package liblpsolve55-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on lzma-dev; however: Package lzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-serialization-dev; however: Package libboost-serialization-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libmysql++-dev; however: Package libmysql++-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} default-libmysqlclient-dev{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libamd2{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization-dev{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libbtf1{a} libbz2-dev{a} libcamd2{a} libccolamd2{a} libcholmod3{a} libcolamd2{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libcxsparse3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgraphblas3{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libicu-dev{a} libicu67{a} libklu1{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libldl2{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmariadb-dev{a} libmariadb-dev-compat{a} libmariadb3{a} libmd0{a} libmetis5{a} libmongoose2{a} libmpdec3{a} libmysql++-dev{a} libmysql++3v5{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librbio2{a} libreadline8{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsliplu1{a} libspqr2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparseconfig5{a} libtool{a} libuchardet0{a} libumfpack5{a} libxml2{a} libyaml-0-2{a} lzma-dev{a} m4{a} man-db{a} mariadb-common{a} media-types{a} mysql-common{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget zip 0 packages upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 87.8 MB of archives. After unpacking 602 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1k-1 [860 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 rubygems-integration all 1.18 [6704 B] Get: 26 http://deb.debian.org/debian bullseye/main i386 rake all 13.0.3-1 [84.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libyaml-0-2 i386 0.2.2-1 [51.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libruby2.7 i386 2.7.3-2 [4305 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 ruby2.7 i386 2.7.3-2 [744 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 ruby-rubygems all 3.2.5-2 [281 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 ruby i386 1:2.7+2 [11.7 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 asciidoctor all 2.0.12-2 [83.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 mysql-common all 5.8+1.0.7 [7464 B] Get: 64 http://deb.debian.org/debian bullseye/main i386 mariadb-common all 1:10.5.10-2 [36.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libmariadb3 i386 1:10.5.10-2 [173 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libssl-dev i386 1.1.1k-1 [1841 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libmariadb-dev i386 1:10.5.10-2 [183 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libmariadb-dev-compat i386 1:10.5.10-2 [34.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 default-libmysqlclient-dev i386 1.0.7 [3932 B] Get: 71 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-7 [209 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libsuitesparseconfig5 i386 1:5.8.1+dfsg-2 [23.1 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libamd2 i386 1:5.8.1+dfsg-2 [30.7 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libbamtools2.5.1 i386 2.5.1+dfsg-9 [176 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libbamtools-dev i386 2.5.1+dfsg-9 [230 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libblas-dev i386 3.9.0-3 [157 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74.0 i386 1.74.0-9 [542 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-7 [9801 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74-dev i386 1.74.0-9 [618 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams1.74-dev i386 1.74.0-9 [275 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 84 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74.0 i386 1.74.0-9 [346 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74-dev i386 1.74.0-9 [390 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libboost-serialization-dev i386 1.74.0.3 [4560 B] Get: 87 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libbtf1 i386 1:5.8.1+dfsg-2 [23.6 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libcamd2 i386 1:5.8.1+dfsg-2 [31.2 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libccolamd2 i386 1:5.8.1+dfsg-2 [32.1 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libcolamd2 i386 1:5.8.1+dfsg-2 [27.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libmetis5 i386 5.1.0.dfsg-7 [171 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libcholmod3 i386 1:5.8.1+dfsg-2 [242 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3+b1 [471 kB] Get: 106 http://deb.debian.org/debian bullseye/main i386 libcxsparse3 i386 1:5.8.1+dfsg-2 [64.3 kB] Get: 107 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 108 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libgraphblas3 i386 1:5.8.1+dfsg-2 [6146 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libgslcblas0 i386 2.6+dfsg-2 [99.2 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 libgsl25 i386 2.6+dfsg-2 [911 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 libgsl-dev i386 2.6+dfsg-2 [1146 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 115 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 libklu1 i386 1:5.8.1+dfsg-2 [57.5 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 liblapack-dev i386 3.9.0-3 [3759 kB] Get: 118 http://deb.debian.org/debian bullseye/main i386 libldl2 i386 1:5.8.1+dfsg-2 [23.4 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 libmongoose2 i386 1:5.8.1+dfsg-2 [49.4 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 libumfpack5 i386 1:5.8.1+dfsg-2 [156 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 librbio2 i386 1:5.8.1+dfsg-2 [34.4 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 libspqr2 i386 1:5.8.1+dfsg-2 [83.5 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libsliplu1 i386 1:5.8.1+dfsg-2 [56.5 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 libsuitesparse-dev i386 1:5.8.1+dfsg-2 [6444 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 liblpsolve55-dev i386 5.5.2.5-2 [446 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 libmysql++3v5 i386 3.2.5-2 [170 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 libmysql++-dev i386 3.2.5-2 [149 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 libncurses-dev i386 6.2+20201114-2 [373 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libncurses5-dev i386 6.2+20201114-2 [932 B] Get: 131 http://deb.debian.org/debian bullseye/main i386 libsqlite3-dev i386 3.34.1-3 [1001 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 lzma-dev all 9.22-2.2 [44.8 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] Fetched 87.8 MB in 2s (55.8 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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../3-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:i386. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_i386.deb ... Unpacking libpython3.9-minimal:i386 (3.9.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../6-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_i386.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:i386 (3.9.2-1) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:i386. Preparing to unpack .../2-libmpdec3_2.5.1-1_i386.deb ... Unpacking libmpdec3:i386 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../4-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:i386. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20963 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_1.1.1k-1_i386.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../005-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../008-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../009-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../010-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../011-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../012-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../013-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../014-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../015-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../016-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../017-libedit2_3.1-20191231-2+b1_i386.deb ... Unpacking libedit2:i386 (3.1-20191231-2+b1) ... Selecting previously unselected package libyaml-0-2:i386. Preparing to unpack .../018-libyaml-0-2_0.2.2-1_i386.deb ... Unpacking libyaml-0-2:i386 (0.2.2-1) ... Selecting previously unselected package libruby2.7:i386. Preparing to unpack .../019-libruby2.7_2.7.3-2_i386.deb ... Unpacking libruby2.7:i386 (2.7.3-2) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../020-ruby2.7_2.7.3-2_i386.deb ... Unpacking ruby2.7 (2.7.3-2) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../021-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../022-ruby_1%3a2.7+2_i386.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../023-ruby-asciidoctor_2.0.12-2_all.deb ... Unpacking ruby-asciidoctor (2.0.12-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../024-asciidoctor_2.0.12-2_all.deb ... Unpacking asciidoctor (2.0.12-2) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../025-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../026-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../027-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../028-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../029-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../030-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../031-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../032-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../033-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../034-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../035-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../036-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../037-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../038-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../039-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../040-libicu67_67.1-7_i386.deb ... Unpacking libicu67:i386 (67.1-7) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../041-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../042-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../043-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../044-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../045-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package mysql-common. Preparing to unpack .../046-mysql-common_5.8+1.0.7_all.deb ... Unpacking mysql-common (5.8+1.0.7) ... Selecting previously unselected package mariadb-common. Preparing to unpack .../047-mariadb-common_1%3a10.5.10-2_all.deb ... Unpacking mariadb-common (1:10.5.10-2) ... Selecting previously unselected package libmariadb3:i386. Preparing to unpack .../048-libmariadb3_1%3a10.5.10-2_i386.deb ... Unpacking libmariadb3:i386 (1:10.5.10-2) ... Selecting previously unselected package libssl-dev:i386. Preparing to unpack .../049-libssl-dev_1.1.1k-1_i386.deb ... Unpacking libssl-dev:i386 (1.1.1k-1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../050-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libmariadb-dev. Preparing to unpack .../051-libmariadb-dev_1%3a10.5.10-2_i386.deb ... Unpacking libmariadb-dev (1:10.5.10-2) ... Selecting previously unselected package libmariadb-dev-compat:i386. Preparing to unpack .../052-libmariadb-dev-compat_1%3a10.5.10-2_i386.deb ... 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Unpacking libmongoose2:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libumfpack5:i386. Preparing to unpack .../103-libumfpack5_1%3a5.8.1+dfsg-2_i386.deb ... Unpacking libumfpack5:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package librbio2:i386. Preparing to unpack .../104-librbio2_1%3a5.8.1+dfsg-2_i386.deb ... Unpacking librbio2:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libspqr2:i386. Preparing to unpack .../105-libspqr2_1%3a5.8.1+dfsg-2_i386.deb ... Unpacking libspqr2:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libsliplu1:i386. Preparing to unpack .../106-libsliplu1_1%3a5.8.1+dfsg-2_i386.deb ... Unpacking libsliplu1:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package libsuitesparse-dev:i386. Preparing to unpack .../107-libsuitesparse-dev_1%3a5.8.1+dfsg-2_i386.deb ... Unpacking libsuitesparse-dev:i386 (1:5.8.1+dfsg-2) ... Selecting previously unselected package liblpsolve55-dev. 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Selecting previously unselected package libsqlite3-dev:i386. Preparing to unpack .../114-libsqlite3-dev_3.34.1-3_i386.deb ... Unpacking libsqlite3-dev:i386 (3.34.1-3) ... Selecting previously unselected package lzma-dev. Preparing to unpack .../115-lzma-dev_9.22-2.2_all.deb ... Unpacking lzma-dev (9.22-2.2) ... Selecting previously unselected package samtools. Preparing to unpack .../116-samtools_1.11-1_i386.deb ... Unpacking samtools (1.11-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libgraphblas3:i386 (1:5.8.1+dfsg-2) ... Setting up mysql-common (5.8+1.0.7) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-7) ... Setting up libgslcblas0:i386 (2.6+dfsg-2) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libgsl25:i386 (2.6+dfsg-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.2-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libldl2:i386 (1:5.8.1+dfsg-2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up libmetis5:i386 (5.1.0.dfsg-7) ... Setting up file (1:5.39-3) ... Setting up libbtf1:i386 (1:5.8.1+dfsg-2) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up mariadb-common (1:10.5.10-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libsqlite3-dev:i386 (3.34.1-3) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libboost-regex1.74.0:i386 (1.74.0-9) ... Setting up libbamtools2.5.1:i386 (2.5.1+dfsg-9) ... Setting up libssl-dev:i386 (1.1.1k-1) ... Setting up autopoint (0.21-4) ... Setting up icu-devtools (67.1-7) ... Setting up libmariadb3:i386 (1:10.5.10-2) ... Setting up libmysql++3v5:i386 (3.2.5-2) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up libboost-serialization1.74.0:i386 (1.74.0-9) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up libcxsparse3:i386 (1:5.8.1+dfsg-2) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up libdeflate-dev:i386 (1.7-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libicu-dev:i386 (67.1-7) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libsuitesparseconfig5:i386 (1:5.8.1+dfsg-2) ... Setting up libblas-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up librbio2:i386 (1:5.8.1+dfsg-2) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libamd2:i386 (1:5.8.1+dfsg-2) ... Setting up liblapack3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libncurses-dev:i386 (6.2+20201114-2) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libcolamd2:i386 (1:5.8.1+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:i386 (3.1-20191231-2+b1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:i386 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libsliplu1:i386 (1:5.8.1+dfsg-2) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libcamd2:i386 (1:5.8.1+dfsg-2) ... Setting up libmongoose2:i386 (1:5.8.1+dfsg-2) ... Setting up libbamtools-dev:i386 (2.5.1+dfsg-9) ... Setting up liblapack-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up lzma-dev (9.22-2.2) ... Setting up autoconf (2.69-14) ... Setting up libboost-serialization1.74-dev:i386 (1.74.0-9) ... Setting up libmariadb-dev (1:10.5.10-2) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0-9) ... Setting up groff-base (1.22.4-6) ... Setting up libklu1:i386 (1:5.8.1+dfsg-2) ... Setting up libccolamd2:i386 (1:5.8.1+dfsg-2) ... Setting up libncurses5-dev:i386 (6.2+20201114-2) ... Setting up libcholmod3:i386 (1:5.8.1+dfsg-2) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libmariadb-dev-compat:i386 (1:10.5.10-2) ... Setting up libspqr2:i386 (1:5.8.1+dfsg-2) ... Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:i386 (1.11-4) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libumfpack5:i386 (1:5.8.1+dfsg-2) ... Setting up libboost-serialization-dev:i386 (1.74.0.3) ... Setting up python3.9 (3.9.2-1) ... Setting up default-libmysqlclient-dev:i386 (1.0.7) ... Setting up libsuitesparse-dev:i386 (1:5.8.1+dfsg-2) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Setting up libmysql++-dev:i386 (3.2.5-2) ... Setting up liblpsolve55-dev (5.5.2.5-2) ... Setting up rake (13.0.3-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up libruby2.7:i386 (2.7.3-2) ... Setting up ruby2.7 (2.7.3-2) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (3988 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 ... 41883 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 I: Running cd /build/augustus-3.4.0+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.4.0+dfsg2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' cd src; make clean make[3]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o sqliteDB.o rm -f ../../../bin/homGeneMapping make[3]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' cd ../..; tests/auxprogs/homGeneMapping/test_homGeneMapping.py --clean make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' rm -rf *.o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' rm -f bam2wig bam2wig.o bam2wig rm -f ../../bin/bam2wig cd ../..; tests/auxprogs/bam2wig/test_bam2wig.py --clean make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o rm -f filterBam rm -f ../../../bin/filterBam make[3]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' rm -rf bin rm -f debian/*substvars rm -f debian/mansrc/*.1 find . -name "__pycache__" | xargs -r rm -r find src -name "*.o" | xargs -r rm find auxprogs -name "*.o" | xargs -r rm rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c In file included from /usr/include/string.h:495, from aln2wig.c:15: In function 'strncpy', inlined from 'main' at aln2wig.c:454:6: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'main' at aln2wig.c:460:6: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'main' at aln2wig.c:327:6: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'main' at aln2wig.c:334:6: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o mkdir -p ../../bin cp aln2wig ../../bin make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' g++ -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools g++ -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp bam2hints ../../bin make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' cc -Wall -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2wig.c -o bam2wig.o -I/usr/include/htslib bam2wig.c: In function 'main': bam2wig.c:172:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 172 | printf("%ld %d\n", pos+1, coverage); | ~~^ ~~~~~ | | | | long int hts_pos_t {aka long long int} | %lld cc -Wall -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig -lhts -lz -lpthread mkdir -p ../../bin cp bam2wig ../../bin/bam2wig make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c compileSpliceCands.c: In function 'getChromosome': compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90 226 | s = malloc(3500000000); | ^ In file included from /usr/include/string.h:495, from compileSpliceCands.c:12: In function 'strncat', inlined from 'getChromosome' at compileSpliceCands.c:216:2: /usr/include/i386-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function 'getChromosome': compileSpliceCands.c:216:2: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:226:6: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 226 | s = malloc(3500000000); | ^~~~~~~~~~~~~~~~~~ In file included from compileSpliceCands.c:14: /usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here 539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ In file included from /usr/include/string.h:495, from compileSpliceCands.c:12: In function 'strncpy', inlined from 'parseLine' at compileSpliceCands.c:292:2: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function 'parseList': compileSpliceCands.c:350:36: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized] 350 | findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand); | ~~~~^~~~~~ compileSpliceCands.c: In function 'main': compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o cp compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wl,-z,relro -Wl,-z,now -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3 mkdir -p ../../../bin/ cp homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' g++ -c -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 joingenes.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_transcript.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_ios.cpp In file included from /usr/include/string.h:495, from jg_transcript.h:5, from jg_ios.cpp:1: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)' at jg_ios.cpp:251:14: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)' at jg_ios.cpp:79:14: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)' at jg_ios.cpp:148:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 300 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now joingenes.o jg_transcript.o jg_ios.o -o joingenes mkdir -p ../../bin/ cp joingenes ../../bin/ make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' dh_auto_build make -j18 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.4.0+dfsg2' mkdir -p bin cd src && make make[3]: Entering directory '/build/augustus-3.4.0+dfsg2/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../include/types.hh:34, from ../include/hints.hh:12, from hints.cc:10: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'std::istream& operator>>(std::istream&, Feature&)' at hints.cc:82:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags cp prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp load2sqlitedb ../bin/ cp load2db ../bin/ cp pp_simScore ../bin/ cp fastBlockSearch ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp getSeq ../bin/ cp etraining ../bin/ cp augustus ../bin/ make[3]: Leaving directory '/build/augustus-3.4.0+dfsg2/src' cd auxprogs && make make[3]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs' cd aln2wig; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'aln2wig' is up to date. make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/aln2wig' cd bam2hints; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2hints' is up to date. make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'compileSpliceCands' is up to date. make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[5]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/build/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/joingenes' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building file: ../src/Compute_UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" Finished building: ../src/Compute_UTRs.cpp Building file: ../src/Coord_Transform.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" Finished building: ../src/Coord_Transform.cpp Building file: ../src/Genomic_Data.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" Finished building: ../src/Genomic_Data.cpp Building file: ../src/Splice_Sites.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" Finished building: ../src/Splice_Sites.cpp Building file: ../src/Supporting_Methods.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" Finished building: ../src/Supporting_Methods.cpp Building file: ../src/Test.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp" Finished building: ../src/Test.cpp Building file: ../src/UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp" Finished building: ../src/UTRs.cpp Building file: ../src/main.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp" Finished building: ../src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o Finished building target: utrrnaseq make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug' cd bam2wig; make; make[4]: Entering directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2wig' is up to date. make[4]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs/bam2wig' make[3]: Leaving directory '/build/augustus-3.4.0+dfsg2/auxprogs' make[2]: Leaving directory '/build/augustus-3.4.0+dfsg2' asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' dh_auto_test make -j18 test make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' cd tests/examples && ./testcases.py --html test_utr_on (__main__.TestAugustus) ... ok test_hints_MPE (__main__.TestAugustus) ... ok test_training_new_species (__main__.TestAugustus) ... ok test_ab_initio_prediction (__main__.TestAugustus) ... ok test_format_and_error_out (__main__.TestAugustus) ... ok test_cgp (__main__.TestAugustus) ... ok test_cgp_sqlite (__main__.TestAugustus) ... ok test_cgp_sqlite_hints (__main__.TestAugustus) ... ok ---------------------------------------------------------------------- Ran 8 tests in 419.005s OK Removing generated test files... ---------------------------------------------------------------------- Executing small test suite ---------------------------------------------------------------------- Creating SQLite database for cgp test cases... tests/auxprogs/bam2wig/test_bam2wig.py --html test_bam2wig (__main__.TestBam2Wig) ... ok test_bam2wig_region (__main__.TestBam2Wig) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.025s OK make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \ debian/augustus/usr/share/augustus/scripts/*.txt chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus cp docs/README* debian/augustus-doc/usr/share/doc/augustus cp docs/EXONCAND-MSAS-CGP.md \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial-cgp \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/augustus-3.4.0+dfsg2' dh_compress -Xtutorial make[1]: Leaving directory '/build/augustus-3.4.0+dfsg2' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'augustus' in '../augustus_3.4.0+dfsg2-2_i386.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.4.0+dfsg2-2_all.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.4.0+dfsg2-2_i386.deb'. dpkg-deb: building package 'augustus-data' in '../augustus-data_3.4.0+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../augustus_3.4.0+dfsg2-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/45565/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/45565/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/45565 and its subdirectories I: Current time: Sun Aug 21 02:30:17 +14 2022 I: pbuilder-time-stamp: 1660998617