Sun Apr 28 17:27:28 UTC 2024 I: starting to build augustus/trixie/i386 on jenkins on '2024-04-28 17:27' Sun Apr 28 17:27:28 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/18595/console.log Sun Apr 28 17:27:28 UTC 2024 I: Downloading source for trixie/augustus=3.5.0+dfsg-4 --2024-04-28 17:27:28-- http://deb.debian.org/debian/pool/main/a/augustus/augustus_3.5.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2347 (2.3K) [text/prs.lines.tag] Saving to: ‘augustus_3.5.0+dfsg-4.dsc’ 0K .. 100% 313M=0s 2024-04-28 17:27:28 (313 MB/s) - ‘augustus_3.5.0+dfsg-4.dsc’ saved [2347/2347] Sun Apr 28 17:27:28 UTC 2024 I: augustus_3.5.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: augustus Binary: augustus, augustus-data, augustus-doc Architecture: any all Version: 3.5.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://bioinf.uni-greifswald.de/augustus/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/augustus Vcs-Git: https://salsa.debian.org/med-team/augustus.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath Package-List: augustus deb science optional arch=any augustus-data deb science optional arch=all augustus-doc deb doc optional arch=all Checksums-Sha1: a926ee500e46fc39c81376be09bbcca055b8a8ad 151813456 augustus_3.5.0+dfsg.orig.tar.xz 6a69caecfd6f16557523333e175bf2a0bbdba35d 20256 augustus_3.5.0+dfsg-4.debian.tar.xz Checksums-Sha256: 30a2a5200e7201a28383bebb98350eab9e043e38d0f7b825a1c8a614a6e68dc8 151813456 augustus_3.5.0+dfsg.orig.tar.xz dec840e8add73afe43b19f279a5ae9b75d0bf55a2c9036217e1500866d59e68f 20256 augustus_3.5.0+dfsg-4.debian.tar.xz Files: 11cc56baea3047c128e2da42f7cf9dd0 151813456 augustus_3.5.0+dfsg.orig.tar.xz 5968a6a5d5744790b18d5b75f961f648 20256 augustus_3.5.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmVYcaQACgkQ6NN64vCf SHLKQw/+JJQwkkd7EXC82qHyLez1uhzU/OwI+zAYcZhlznX50phxu/Bl+Kz3Uz+6 uVj2G2nvqIYzHBqLYewxeSJtpeYFT1fDeDQJn4fkHVT4JS346IZfF+vMGfu20t21 clNrN0Bgl+jrSRmhqkLoeNgEXdm00CYb9aiv397+Yjuls5jGLGXLucrPDS2iyQiv L8ZVpo13vkqODPiQ20um2IGF9U97bPDZx6NNlV+JsB8AtTk0YI3rb9tE5/fZFzcq npVjvtC5r2lXPrukbfSjtyTfG73eiPCb306QoeKb24adbkzm8CkVOuY2wbYX7jjt 0OilhRpFL2kLqKjhMZsvs6lNfjFdGk7uiQhMryxHx3LrE2oOkwGuu3y/ViDQLbjr toUzsFrzsA+wo9+DTr4cLWlQVs8FzexIgqEcoV85/rpsIL/FfaE3gSQ4rXhplI0H hBs/RUJMeo51r3kf7kPe/KDCfJQOdI7wFcRQ7LbNHqUK4H9l5rxLVZ6jBYQhSjTr thXgQZiLlq/SuzvQptoQthQYdDQjOnY0jHpUdcAaLz8eu0E7AcwAEGMU3RhxvhaG 63Toww3+/ULo27kAudNGlHYyOXGGgAuxkXTx5g4Ozx5W2SJEjnezhRnxfID3NY8y WCVfgkkmJ+GRRTo2mxIflq+1GqPtJefanilm1nj5Zc3bIQ8njgs= =1x+C -----END PGP SIGNATURE----- Sun Apr 28 17:27:28 UTC 2024 I: Checking whether the package is not for us Sun Apr 28 17:27:28 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Sun Apr 28 17:27:28 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Sun Apr 28 17:47:08 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 05:27:34 -12 2024 I: pbuilder-time-stamp: 1714325254 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [augustus_3.5.0+dfsg-4.dsc] I: copying [./augustus_3.5.0+dfsg.orig.tar.xz] I: copying [./augustus_3.5.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 18 08:11:16 2023 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting augustus in augustus-3.5.0+dfsg dpkg-source: info: unpacking augustus_3.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking augustus_3.5.0+dfsg-4.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 dpkg-source: info: applying s390x-disable-filterbam-tests.patch dpkg-source: info: applying cstdint.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/42949/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='76873c1b387e447a81e4050863d39435' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='42949' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/pbuilderrc_0FBW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/b1 --logfile b1/build.log augustus_3.5.0+dfsg-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:12 /bin -> usr/bin I: user script /srv/workspace/pbuilder/42949/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, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19884 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 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. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} chrpath{a} debhelper{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} libamd3{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost1.83-dev{a} libbtf2{a} libbz2-dev{a} libcamd3{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcxsparse4{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu-dev{a} libicu72{a} libklu2{a} liblapack-dev{a} liblapack3{a} libldl3{a} liblpsolve55-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libparu0{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librbio4{a} libreadline8t64{a} libspex3{a} libspqr4{a} libsqlite3-dev{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libtool{a} libuchardet0{a} libumfpack6{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libgpm2 libgraphblas-dev libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 65.2 MB of archives. After unpacking 389 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev but it is not installable Depends: libssl-dev but it is not installable Depends: libmysql++-dev but it is not installable Depends: asciidoctor but it is not installable Depends: samtools but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libssl3 [3.1.5-1 (now)] Install the following packages: 2) asciidoctor [2.0.20-1 (testing)] 3) ca-certificates [20240203 (testing)] 4) default-libmysqlclient-dev [1.1.0+b1 (testing)] 5) libbrotli1 [1.1.0-2+b3 (testing)] 6) libbsd0 [0.12.2-1 (testing)] 7) libcurl3t64-gnutls [8.7.1-3 (testing)] 8) libcurl4-gnutls-dev [8.7.1-3 (testing)] 9) libdeflate-dev [1.20-1 (testing)] 10) libdeflate0 [1.20-1 (testing)] 11) libedit2 [3.1-20230828-1+b1 (testing)] 12) libhts-dev [1.19+ds-1 (testing)] 13) libhts3 [1.19+ds-1 (testing)] 14) libhtscodecs2 [1.6.0-1+b1 (testing)] 15) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 16) liblzma-dev [5.6.1+really5.4.5-1 (testing)] 17) libmariadb-dev [1:10.11.6-2 (testing)] 18) libmariadb-dev-compat [1:10.11.6-2 (testing)] 19) libmariadb3 [1:10.11.6-2 (testing)] 20) libmysql++-dev [3.2.5-2.3 (testing)] 21) libmysql++3t64 [3.2.5-2.3 (testing)] 22) libnghttp2-14 [1.59.0-1 (testing)] 23) libpsl5t64 [0.21.2-1.1 (testing)] 24) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 25) libruby [1:3.1 (testing)] 26) libruby3.1 [3.1.2-8 (testing)] 27) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 28) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 29) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 30) libssl-dev [3.2.1-3 (testing)] 31) libssl3t64 [3.2.1-3 (testing)] 32) libyaml-0-2 [0.2.5-1+b1 (testing)] 33) mariadb-common [1:10.11.6-2 (testing)] 34) mysql-common [5.8+1.1.0 (testing)] 35) openssl [3.2.1-3 (testing)] 36) rake [13.0.6-3 (testing)] 37) ruby [1:3.1 (testing)] 38) ruby-asciidoctor [2.0.20-1 (testing)] 39) ruby-net-telnet [0.2.0-1 (testing)] 40) ruby-rubygems [3.4.20-1 (testing)] 41) ruby-sdbm [1.0.0-5+b2 (testing)] 42) ruby-webrick [1.8.1-1 (testing)] 43) ruby-xmlrpc [0.3.2-2 (testing)] 44) ruby3.1 [3.1.2-8 (testing)] 45) rubygems-integration [1.18 (testing)] 46) samtools [1.19.2-1 (testing)] The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{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} libamd3{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbsd0{a} libbtf2{a} libbz2-dev{a} libcamd3{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcxsparse4{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libklu2{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl3{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmariadb-dev{a} libmariadb-dev-compat{a} libmariadb3{a} libmysql++-dev{a} libmysql++3t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libparu0{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librbio4{a} libreadline8t64{a} librtmp1{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libspex3{a} libspqr4{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libssl3t64{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libtool{a} libuchardet0{a} libumfpack6{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mariadb-common{a} media-types{a} mysql-common{a} netbase{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages will be REMOVED: libssl3{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libgpm2 libgraphblas-dev libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget zip 0 packages upgraded, 132 newly installed, 1 to remove and 0 not upgraded. Need to get 85.1 MB of archives. After unpacking 453 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libssl3t64 i386 3.2.1-3 [2234 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-3 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 14 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 openssl i386 3.2.1-3 [1364 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 rubygems-integration all 1.18 [6704 B] Get: 28 http://deb.debian.org/debian trixie/main i386 rake all 13.0.6-3 [83.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libruby i386 1:3.1 [4968 B] Get: 33 http://deb.debian.org/debian trixie/main i386 ruby-sdbm i386 1.0.0-5+b2 [16.7 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20230828-1+b1 [97.8 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240414-1 [112 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-1+b1 [55.2 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libruby3.1 i386 3.1.2-8 [5456 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 ruby3.1 i386 3.1.2-8 [663 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 ruby-rubygems all 3.4.20-1 [309 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 ruby i386 1:3.1 [5872 B] Get: 42 http://deb.debian.org/debian trixie/main i386 ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 asciidoctor all 2.0.20-1 [87.7 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 chrpath i386 0.16-2+b1 [17.5 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 57 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 mysql-common all 5.8+1.1.0 [6636 B] Get: 66 http://deb.debian.org/debian trixie/main i386 mariadb-common all 1:10.11.6-2 [25.2 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libmariadb3 i386 1:10.11.6-2 [174 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.2.1-3 [2744 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libmariadb-dev i386 1:10.11.6-2 [267 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libmariadb-dev-compat i386 1:10.11.6-2 [24.0 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 default-libmysqlclient-dev i386 1.1.0+b1 [3392 B] Get: 73 http://deb.debian.org/debian trixie/main i386 icu-devtools i386 72.1-4+b1 [216 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libsuitesparseconfig7 i386 1:7.7.0+dfsg-2 [22.7 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libamd3 i386 1:7.7.0+dfsg-2 [41.6 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-5 [175 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-5 [240 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3 [152 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-2+b2 [10.6 MB] Get: 81 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83.0 i386 1.83.0-2+b2 [328 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libicu-dev i386 72.1-4+b1 [10.6 MB] Get: 83 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83-dev i386 1.83.0-2+b2 [347 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libboost-iostreams1.83-dev i386 1.83.0-2+b2 [264 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B] Get: 86 http://deb.debian.org/debian trixie/main i386 libboost-serialization1.83.0 i386 1.83.0-2+b2 [341 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libboost-serialization1.83-dev i386 1.83.0-2+b2 [383 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libboost-serialization-dev i386 1.83.0.2+b2 [3832 B] Get: 89 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libbtf2 i386 1:7.7.0+dfsg-2 [24.4 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-5.1 [31.4 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libcamd3 i386 1:7.7.0+dfsg-2 [39.5 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libccolamd3 i386 1:7.7.0+dfsg-2 [42.1 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libcolamd3 i386 1:7.7.0+dfsg-2 [34.1 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libcholmod5 i386 1:7.7.0+dfsg-2 [714 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.7.1-3 [467 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.7.1-3 [589 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libcxsparse4 i386 1:7.7.0+dfsg-2 [99.3 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.7.1+dfsg-6+b1 [97.7 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libgsl27 i386 2.7.1+dfsg-6+b1 [920 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.7.1+dfsg-6+b1 [1169 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.1+really5.4.5-1 [304 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libklu2 i386 1:7.7.0+dfsg-2 [91.5 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3 [4400 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libldl3 i386 1:7.7.0+dfsg-2 [23.6 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libsuitesparse-mongoose3 i386 1:7.7.0+dfsg-2 [52.8 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libumfpack6 i386 1:7.7.0+dfsg-2 [308 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 librbio4 i386 1:7.7.0+dfsg-2 [43.7 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libspqr4 i386 1:7.7.0+dfsg-2 [159 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libspex3 i386 1:7.7.0+dfsg-2 [66.1 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libparu0 i386 1:7.7.0+dfsg-2 [76.2 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libsuitesparse-dev i386 1:7.7.0+dfsg-2 [1673 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 liblpsolve55-dev i386 5.5.2.5-2+b1 [461 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libmysql++3t64 i386 3.2.5-2.3 [163 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libmysql++-dev i386 3.2.5-2.3 [145 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libncurses-dev i386 6.4+20240414-1 [380 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 libsqlite3-dev i386 3.45.1-1 [1171 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 samtools i386 1.19.2-1 [680 kB] Fetched 85.1 MB in 2s (44.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:i386: dependency problems, but removing anyway as you requested: libkrb5-3:i386 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19884 files and directories currently installed.) Removing libssl3:i386 (3.1.5-1) ... Selecting previously unselected package libssl3t64:i386. (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 ... 19871 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_i386.deb ... Unpacking libssl3t64:i386 (3.2.1-3) ... Setting up libssl3t64:i386 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19886 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20202 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../5-libreadline8t64_8.2-4_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21196 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.2.1-3_i386.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../005-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-3+b1_i386.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../011-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../013-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... 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Preparing to unpack .../111-libparu0_1%3a7.7.0+dfsg-2_i386.deb ... Unpacking libparu0:i386 (1:7.7.0+dfsg-2) ... Selecting previously unselected package libsuitesparse-dev:i386. Preparing to unpack .../112-libsuitesparse-dev_1%3a7.7.0+dfsg-2_i386.deb ... Unpacking libsuitesparse-dev:i386 (1:7.7.0+dfsg-2) ... Selecting previously unselected package liblpsolve55-dev. Preparing to unpack .../113-liblpsolve55-dev_5.5.2.5-2+b1_i386.deb ... Unpacking liblpsolve55-dev (5.5.2.5-2+b1) ... Selecting previously unselected package libmysql++3t64:i386. Preparing to unpack .../114-libmysql++3t64_3.2.5-2.3_i386.deb ... Unpacking libmysql++3t64:i386 (3.2.5-2.3) ... Selecting previously unselected package libmysql++-dev:i386. Preparing to unpack .../115-libmysql++-dev_3.2.5-2.3_i386.deb ... Unpacking libmysql++-dev:i386 (3.2.5-2.3) ... Selecting previously unselected package libncurses-dev:i386. Preparing to unpack .../116-libncurses-dev_6.4+20240414-1_i386.deb ... Unpacking libncurses-dev:i386 (6.4+20240414-1) ... Selecting previously unselected package libsqlite3-dev:i386. Preparing to unpack .../117-libsqlite3-dev_3.45.1-1_i386.deb ... Unpacking libsqlite3-dev:i386 (3.45.1-1) ... Selecting previously unselected package samtools. Preparing to unpack .../118-samtools_1.19.2-1_i386.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:i386 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-2) ... Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libboost1.83-dev:i386 (1.83.0-2+b2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libgslcblas0:i386 (2.7.1+dfsg-6+b1) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1+b1) ... Setting up libboost-regex1.83.0:i386 (1.83.0-2+b2) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up libpsl5t64:i386 (0.21.2-1.1) ... Setting up libnghttp2-14:i386 (1.59.0-1) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up libdeflate0:i386 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:i386 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up libldl3:i386 (1:7.7.0+dfsg-2) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:i386 (0.191-1+b1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 28 17:28:41 UTC 2024. Universal Time is now: Sun Apr 28 17:28:41 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:10.11.6-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libboost-serialization1.83.0:i386 (1.83.0-2+b2) ... Setting up libbtf2:i386 (1:7.7.0+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... 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 (3.45.1-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:i386 (6.4+20240414-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libssl-dev:i386 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up icu-devtools (72.1-4+b1) ... Setting up libmariadb3:i386 (1:10.11.6-2) ... Setting up libbamtools2.5.2:i386 (2.5.2+dfsg-5) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:i386 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:i386 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsuitesparseconfig7:i386 (1:7.7.0+dfsg-2) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libssh2-1t64:i386 (1.11.0-4.1+b2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up libdeflate-dev:i386 (1.20-1) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:i386 (72.1-4+b1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:i386 (3.12.0-3) ... 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 libbz2-dev:i386 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libmysql++3t64:i386 (3.2.5-2.3) ... Setting up liblapack3:i386 (3.12.0-3) ... 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 (6.4+20240414-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libamd3:i386 (1:7.7.0+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:i386 (1:7.7.0+dfsg-2) ... Setting up libspex3:i386 (1:7.7.0+dfsg-2) ... Setting up libsuitesparse-mongoose3:i386 (1:7.7.0+dfsg-2) ... Setting up libedit2:i386 (3.1-20230828-1+b1) ... Setting up libcxsparse4:i386 (1:7.7.0+dfsg-2) ... Setting up libboost-serialization1.83-dev:i386 (1.83.0-2+b2) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Setting up libcamd3:i386 (1:7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up librbio4:i386 (1:7.7.0+dfsg-2) ... Setting up libbamtools-dev:i386 (2.5.2+dfsg-5) ... Setting up liblapack-dev:i386 (3.12.0-3) ... 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 libboost-regex1.83-dev:i386 (1.83.0-2+b2) ... Setting up libboost-serialization-dev:i386 (1.83.0.2+b2) ... Setting up libccolamd3:i386 (1:7.7.0+dfsg-2) ... Setting up libmariadb-dev (1:10.11.6-2) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libmariadb-dev-compat (1:10.11.6-2) ... Setting up libcholmod5:i386 (1:7.7.0+dfsg-2) ... Setting up libspqr4:i386 (1:7.7.0+dfsg-2) ... Setting up libboost-iostreams1.83-dev:i386 (1.83.0-2+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up libcurl3t64-gnutls:i386 (8.7.1-3) ... Setting up rubygems-integration (1.18) ... Setting up libboost-iostreams-dev:i386 (1.83.0.2+b2) ... Setting up libcurl4-gnutls-dev:i386 (8.7.1-3) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libklu2:i386 (1:7.7.0+dfsg-2) ... Setting up libumfpack6:i386 (1:7.7.0+dfsg-2) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up default-libmysqlclient-dev:i386 (1.1.0+b1) ... Setting up python3.11 (3.11.8-1) ... Setting up libhts3:i386 (1.19+ds-1) ... Setting up libhts-dev:i386 (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up libparu0:i386 (1:7.7.0+dfsg-2) ... Setting up python3 (3.11.6-1) ... Setting up samtools (1.19.2-1) ... Setting up libmysql++-dev:i386 (3.2.5-2.3) ... Setting up libsuitesparse-dev:i386 (1:7.7.0+dfsg-2) ... Setting up liblpsolve55-dev (5.5.2.5-2+b1) ... Setting up libruby:i386 (1:3.1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby (1:3.1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.20-1) ... Setting up ruby-sdbm:i386 (1.0.0-5+b2) ... Setting up libruby3.1:i386 (3.1.2-8) ... Setting up ruby3.1 (3.1.2-8) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for ca-certificates (20240203) ... 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 I: Building the package I: Running cd /build/reproducible-path/augustus-3.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../augustus_3.5.0+dfsg-4_source.changes dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.5.0+dfsg-4 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/reproducible-path/augustus-3.5.0+dfsg' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd src; make clean make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o sqliteDB.o rm -f ../../../bin/homGeneMapping make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean homGeneMapping ; fi make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' rm -f *.o joingenes ../../bin/joingenes make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' rm -f aln2wig aln2wig.o ../../bin/aln2wig make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' rm -f bam2wig.o bam2wig rm -f ../../bin/bam2wig if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean bam2wig ; fi make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' rm -f compileSpliceCands *.o ../../bin/compileSpliceCands make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' rm -f *~ filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o rm -f filterBam rm -f ../../../bin/filterBam make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/utrrnaseq clean make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' rm -rf build/test *.gff rm -rf build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o build/Compute_UTRs.d build/Coord_Transform.d build/Genomic_Data.d build/Splice_Sites.d build/Supporting_Methods.d build/Test.d build/UTRs.d build/main.d build utrrnaseq make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' 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 tests -name "*.sam.bam" | xargs -r rm find auxprogs -name "*.o" | xargs -r rm rm -rf tests/short/examples/results \ tests/short/auxprogs/bam2hints/tmp/ \ tests/short/auxprogs/bam2hints/result_files/ \ tests/short/auxprogs/filterbam/result_files/ rm -f auxprogs/utrrnaseq/Debug/utrrnaseq \ src/augustus \ src/cxxflags \ src/etraining \ src/fastBlockSearch \ src/getSeq \ src/load2db \ src/load2sqlitedb \ src/pp_simScore \ src/prepareAlign make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' 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/reproducible-path/augustus-3.5.0+dfsg' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o mkdir -p ../../bin cp -f aln2wig ../../bin make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/bamtools -c bam2hints.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -I/usr/include/bamtools -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp -f bam2hints ../../bin make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c bam2wig.c: In function 'main': bam2wig.c:172:35: 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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o bam2wig bam2wig.o -lhts -lz -lpthread mkdir -p ../../bin cp -f bam2wig ../../bin/bam2wig make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c compileSpliceCands.c compileSpliceCands.c: In function 'getChromosome': compileSpliceCands.c:226:9: warning: this decimal constant is unsigned only in ISO C90 226 | s = malloc(3500000000); | ^ compileSpliceCands.c:216:9: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=] 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^ compileSpliceCands.c:216:9: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:226:13: 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:553:14: note: in a call to allocation function 'malloc' declared here 553 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ compileSpliceCands.c: In function 'parseLine': compileSpliceCands.c:292:9: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 292 | strncpy(d->name,tokens[0],LINEBUFFER); | ^ compileSpliceCands.c: In function 'parseList': compileSpliceCands.c:333:69: warning: 'left' may be used uninitialized [-Wmaybe-uninitialized] 333 | isCandidate = ((right->averageCoverage>=left->averageCoverage*threshold) || | ~~~~^~~~~~~~~~~~~~~~~ compileSpliceCands.c:314:14: note: 'left' was declared here 314 | Data left; | ^~~~ compileSpliceCands.c: In function 'main': compileSpliceCands.c:563:17: warning: 'chromosomeLength' may be used uninitialized [-Wmaybe-uninitialized] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:416:18: note: 'chromosomeLength' was declared here 416 | long int chromosomeLength; | ^~~~~~~~~~~~~~~~ cc -Wall -pedantic -ansi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o cp -f compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c filterBam.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/initOptions.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c gene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c genome.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -lsqlite3 mkdir -p ../../../bin/ cp -f homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c joingenes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_transcript.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_ios.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o joingenes joingenes.o jg_transcript.o jg_ios.o mkdir -p ../../bin/ cp -f joingenes ../../bin/ make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' dh_auto_build make -j11 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' mkdir -p bin mkdir -p bin cd src && make cd auxprogs && make make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/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/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' cd bam2hints; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc cd compileSpliceCands; make; g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' 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/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc cd filterBam; make; g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc make[5]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/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/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' cd utrrnaseq; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p build Building file: src/Compute_UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Compute_UTRs.d" -MT"build/Compute_UTRs.o" -o "build/Compute_UTRs.o" "src/Compute_UTRs.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc src/Compute_UTRs.cpp: In function 'void compute_UTRs(std::string)': src/Compute_UTRs.cpp:142:18: warning: 'chrom_pos' may be used uninitialized [-Wmaybe-uninitialized] 142 | unsigned chrom_pos; //position for fixedStep only | ^~~~~~~~~ src/Compute_UTRs.cpp:251:69: warning: 'step' may be used uninitialized [-Wmaybe-uninitialized] 251 | for (int i = 0; i < (int)step; ++i) { | ^~~~~~~~~ src/Compute_UTRs.cpp:143:18: note: 'step' was declared here 143 | unsigned step; //Step for fixedStep only | ^~~~ In file included from /usr/include/c++/13/vector:66, from src/Genomic_Data.hpp:9, from src/Compute_UTRs.cpp:5: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Genomic_Data::Scaff_plus_Gen_Data; _Alloc = std::allocator]', inlined from 'void compute_UTRs(std::string)' at src/Compute_UTRs.cpp:199:106: /usr/include/c++/13/bits/stl_vector.h:1126:41: warning: 'idx_former_scaff' may be used uninitialized [-Wmaybe-uninitialized] 1126 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ src/Compute_UTRs.cpp: In function 'void compute_UTRs(std::string)': src/Compute_UTRs.cpp:150:18: note: 'idx_former_scaff' was declared here 150 | unsigned idx_former_scaff; | ^~~~~~~~~~~~~~~~ Finished building: src/Compute_UTRs.cpp Building file: src/Coord_Transform.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/Coord_Transform.o" "src/Coord_Transform.cpp" src/Coord_Transform.cpp:25:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 25 | template struct finding_intron_greater_s : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from src/flex_vec.hpp:8, from src/Coord_Transform.cpp:5: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:33:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 33 | template struct finding_intron_lesser_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:41:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 41 | template struct finding_intron_greater_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:49:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 49 | template struct finding_intron_lesser_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp: In constructor 'Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector*)': src/Coord_Transform.cpp:77:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 77 | bind2nd(finding_intron_greater_s(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:81:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 81 | bind2nd(finding_intron_greater_e(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:89:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 89 | bind2nd(finding_intron_lesser_e(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:93:56: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 93 | bind2nd(finding_intron_lesser_s(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp: In constructor 'Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector*)': src/Coord_Transform.cpp:148:70: warning: 'skip_end' may be used uninitialized [-Wmaybe-uninitialized] 148 | if (skip_start*dir > skip_end*dir) { | ~~~~~~~~^~~~ src/Coord_Transform.cpp:65:13: note: 'skip_end' was declared here 65 | int skip_end; //normally end position + W for this next intron | ^~~~~~~~ Finished building: src/Coord_Transform.cpp Building file: src/Genomic_Data.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc Finished building: src/Genomic_Data.cpp Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc Finished building: src/Splice_Sites.cpp Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc Finished building: src/Supporting_Methods.cpp Building file: src/Test.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc Finished building: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" src/UTRs.cpp:83:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 83 | binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from src/Genomic_Data.hpp:8, from src/UTRs.cpp:5: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:92:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 92 | binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:100:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 100 | template struct finding_intron_greater_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:108:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 108 | template struct finding_intron_lesser_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:116:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 116 | template struct finding_intron_greater_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:124:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 124 | template struct finding_intron_lesser_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:133:49: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 133 | template struct finding_repeat : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp: In static member function 'static unsigned int UTRs::get_max_pos(unsigned int, int, unsigned int, unsigned int, std::vector*)': src/UTRs.cpp:181:64: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_greater; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 181 | bind2nd(finding_coding_region_greater(), pos)) : | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:183:65: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_lesser; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 183 | bind2nd(finding_coding_region_lesser(), pos)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp: In static member function 'static bool UTRs::repeat_in_UTR(unsigned int, unsigned int, std::vector*)': src/UTRs.cpp:196:63: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_repeat; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp: In static member function 'static std::vector UTRs::find_introns_in_range(unsigned int, unsigned int, int, std::vector*)': src/UTRs.cpp:233:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:240:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:252:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:259:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc Finished building: src/UTRs.cpp Building file: src/main.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc Finished building: src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o Finished building target: utrrnaseq make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' cd bam2wig; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' 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/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -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 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f 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 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f load2sqlitedb ../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 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -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 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -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 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -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 -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f load2db ../bin/ cp -f pp_simScore ../bin/ cp -f fastBlockSearch ../bin/ cp -f getSeq ../bin/ cp -f etraining ../bin/ cp -f augustus ../bin/ make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' dh_auto_test make -j11 test make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' mkdir -p bin mkdir -p bin cd src && make cd auxprogs && make make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: 'aln2wig' is up to date. make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' cd bam2hints; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' cd compileSpliceCands; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' cd filterBam; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/joingenes' cd utrrnaseq; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p build make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' cd bam2wig; make; make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' cd tests/short && ./execute_test.py --html examples test_utr_on (examples.test_examples.TestExamples.test_utr_on) ... ok test_hints_MPE (examples.test_examples.TestExamples.test_hints_MPE) ... ok test_training_new_species (examples.test_examples.TestExamples.test_training_new_species) ... ok test_ab_initio_prediction (examples.test_examples.TestExamples.test_ab_initio_prediction) ... ok test_format_and_error_out (examples.test_examples.TestExamples.test_format_and_error_out) ... ok test_cgp (examples.test_examples.TestExamples.test_cgp) ... ok test_cgp_sqlite (examples.test_examples.TestExamples.test_cgp_sqlite) ... ok test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok ---------------------------------------------------------------------- Ran 8 tests in 787.241s OK Removing generated test files... ---------------------------------------------------------------------- Executing small test suite ---------------------------------------------------------------------- Creating SQLite database for cgp test cases... cd tests/short && ./execute_test.py --html bam2hints test_bam2hints (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints) ... ok test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.017s OK cd tests/short && ./execute_test.py --html bam2wig test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig) ... ok test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.047s OK cd tests/short && ./execute_test.py --html filterbam test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok ---------------------------------------------------------------------- Ran 25 tests in 0.711s OK make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' 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/reproducible-path/augustus-3.5.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' chrpath -d debian/*/usr/bin/bam2hints chrpath -d debian/*/usr/bin/filterBam dh_install make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' dh_compress -Xtutorial make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' 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-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-4_i386.deb'. dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-4_i386.deb'. dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-4_all.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.5.0+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../augustus_3.5.0+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../augustus_3.5.0+dfsg-4_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/42949 and its subdirectories I: Current time: Sun Apr 28 05:47:06 -12 2024 I: pbuilder-time-stamp: 1714326426 Sun Apr 28 17:47:08 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Sun Apr 28 17:47:08 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Sun Apr 28 17:59:11 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Sun Apr 28 17:59:12 UTC 2024 I: augustus_3.5.0+dfsg-4_i386.changes: Format: 1.8 Date: Sat, 18 Nov 2023 08:21:25 +0100 Source: augustus Binary: augustus augustus-data augustus-dbgsym augustus-doc Architecture: all i386 Version: 3.5.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: augustus - gene prediction in eukaryotic genomes augustus-data - data files for AUGUSTUS augustus-doc - documentation files for AUGUSTUS Closes: 1043915 Changes: augustus (3.5.0+dfsg-4) unstable; urgency=medium . * Ensure multiple builds can be done in same directory. Done by ensuring the directory is cleaned correctly. Closes: #1043915 Checksums-Sha1: e8f97b6093ec33260c83359c9167e8b069ecf5f0 20263840 augustus-data_3.5.0+dfsg-4_all.deb 88812098c3210976ee0b87919568159b250d79f6 46143328 augustus-dbgsym_3.5.0+dfsg-4_i386.deb f4e24b51f985e464517b40767a7ac40445b5b588 23671260 augustus-doc_3.5.0+dfsg-4_all.deb 13ee7f6c4401130136ea3eb4b3cbddbabda017cc 9438 augustus_3.5.0+dfsg-4_i386.buildinfo c33c92dde8dd669e1e8d380f8bf5e8bdf4dcab3d 2176024 augustus_3.5.0+dfsg-4_i386.deb Checksums-Sha256: d715a3c382ecdc35431d3b0343c65842b93dea90a22dc401c726eff32638550f 20263840 augustus-data_3.5.0+dfsg-4_all.deb ca0654ad7be5efc67672e9011ffcfa6e5a52460cfac66f3459fa4ba800124460 46143328 augustus-dbgsym_3.5.0+dfsg-4_i386.deb cb27e8da343bce5677f52b5ea9208923a02158be71353b6aff6e50165cf616fa 23671260 augustus-doc_3.5.0+dfsg-4_all.deb a5eb940652f8ade203208472eb3fc40c4dd6a3c1e9b6c0ac01b32b4196c1d24f 9438 augustus_3.5.0+dfsg-4_i386.buildinfo 66398eb9298d1277d079945e5d6c0a9f699da5e5c8732964b0506eaeac0dc0bd 2176024 augustus_3.5.0+dfsg-4_i386.deb Files: f7fdf3f6365c1100b62954f7c3b2a6ef 20263840 science optional augustus-data_3.5.0+dfsg-4_all.deb 7794bbd938040703e51941ac63df1d8a 46143328 debug optional augustus-dbgsym_3.5.0+dfsg-4_i386.deb b1983e0b0ce0d1b8e9fabcb118c034ea 23671260 doc optional augustus-doc_3.5.0+dfsg-4_all.deb 0ad0ae580a3af11f331c3a47951c70e6 9438 science optional augustus_3.5.0+dfsg-4_i386.buildinfo 2652572d29595a9f6e5b9237afa5c8e0 2176024 science optional augustus_3.5.0+dfsg-4_i386.deb Sun Apr 28 17:59:13 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-18595.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/augustus_3.5.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/augustus_3.5.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/augustus_3.5.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/b1/augustus_3.5.0+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.Cx48fZOJ/b2/augustus_3.5.0+dfsg-4_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.360s) 1.360s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 1.049s) 1.049s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.668s CPU time consumed: 1.657s Sun Apr 28 17:59:15 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 28 17:59:15 UTC 2024 I: augustus from trixie built successfully and reproducibly on i386. Sun Apr 28 17:59:17 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 28 17:59:17 UTC 2024 I: Submitting 12K b1/augustus_3.5.0+dfsg-4_i386.buildinfo.asc Sun Apr 28 17:59:19 UTC 2024 I: Submitting 12K b2/augustus_3.5.0+dfsg-4_i386.buildinfo.asc Sun Apr 28 17:59:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 28 17:59:20 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 28 17:59:20 UTC 2024 I: Removing signed augustus_3.5.0+dfsg-4_i386.buildinfo.asc files: removed './b1/augustus_3.5.0+dfsg-4_i386.buildinfo.asc' removed './b2/augustus_3.5.0+dfsg-4_i386.buildinfo.asc'