Sat May 25 11:58:00 UTC 2024 I: starting to build augustus/trixie/armhf on jenkins on '2024-05-25 11:57' Sat May 25 11:58:00 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_7/2929/console.log Sat May 25 11:58:00 UTC 2024 I: Downloading source for trixie/augustus=3.5.0+dfsg-4 --2024-05-25 11:58:00-- 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% 301M=0s 2024-05-25 11:58:00 (301 MB/s) - ‘augustus_3.5.0+dfsg-4.dsc’ saved [2347/2347] Sat May 25 11:58:00 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----- Sat May 25 11:58:00 UTC 2024 I: Checking whether the package is not for us Sat May 25 11:58:00 UTC 2024 I: Starting 1st build on remote node virt64b-armhf-rb.debian.net. Sat May 25 11:58:00 UTC 2024 I: Preparing to do remote build '1' on virt64b-armhf-rb.debian.net. Sat May 25 12:47:54 UTC 2024 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 24 23:58:39 -12 2024 I: pbuilder-time-stamp: 1716638319 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: 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/27723/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='be4d0d56834240e8a80501ab79fa98c6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='27723' 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.OpohdMCj/pbuilderrc_XrCa --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.OpohdMCj/b1 --logfile b1/build.log augustus_3.5.0+dfsg-4.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64b 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 23 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27723/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: armhf 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 ... 19445 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: 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} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcxsparse4{a} libdata-optlist-perl{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} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libklu2{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldl3{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmariadb-dev{a} libmariadb-dev-compat{a} libmariadb3{a} libmysql++-dev{a} libmysql++3t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libparams-util-perl{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} libruby3.1t64{a} libspex3{a} libspqr4{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-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 are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato krb5-locales libarchive-cpio-perl libgpm2 libgraphblas-dev libjs-jquery libltdl-dev libmail-sendmail-perl lynx publicsuffix wget zip 0 packages upgraded, 139 newly installed, 0 to remove and 0 not upgraded. Need to get 74.9 MB of archives. After unpacking 411 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.2.1-3 [1326 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.1-1 [85.8 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf rubygems-integration all 1.18 [6704 B] Get: 27 http://deb.debian.org/debian trixie/main armhf rake all 13.0.6-3 [83.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf ruby-sdbm armhf 1.0.0-5+b4 [13.3 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20240517-1 [77.7 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.5-2 [81.8 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-1+b1 [45.5 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libruby3.1t64 armhf 3.1.2-8.3 [5068 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf ruby3.1 armhf 3.1.2-8.3 [663 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 39 http://deb.debian.org/debian trixie/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 41 http://deb.debian.org/debian trixie/main armhf ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf asciidoctor all 2.0.20-1 [87.7 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libparams-util-perl armhf 1.102-3 [23.0 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libsub-install-perl all 0.929-1 [10.5 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libsub-prototype-perl armhf 0.03-2+b2 [9460 B] Get: 58 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.11-1 [10.4 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 61 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf mysql-common all 5.8+1.1.0 [6636 B] Get: 70 http://deb.debian.org/debian trixie/main armhf mariadb-common all 1:10.11.8-1 [26.4 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libmariadb3 armhf 1:10.11.8-1 [159 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.2.1-3 [2348 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libmariadb-dev armhf 1:10.11.8-1 [249 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libmariadb-dev-compat armhf 1:10.11.8-1 [25.2 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf default-libmysqlclient-dev armhf 1.1.0+b1 [3376 B] Get: 77 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-4+b1 [185 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libsuitesparseconfig7 armhf 1:7.7.0+dfsg-2 [21.8 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libamd3 armhf 1:7.7.0+dfsg-2 [39.4 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-5 [139 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libbamtools-dev armhf 2.5.2+dfsg-5 [206 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libblas-dev armhf 3.12.0-3 [119 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-2.1+b1 [10.6 MB] Get: 85 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83.0 armhf 1.83.0-2.1+b1 [307 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-4+b1 [10.1 MB] Get: 87 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83-dev armhf 1.83.0-2.1+b1 [335 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libboost-iostreams1.83-dev armhf 1.83.0-2.1+b1 [260 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libboost-iostreams-dev armhf 1.83.0.2+b2 [3568 B] Get: 90 http://deb.debian.org/debian trixie/main armhf libboost-serialization1.83.0 armhf 1.83.0-2.1+b1 [315 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libboost-serialization1.83-dev armhf 1.83.0-2.1+b1 [385 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libboost-serialization-dev armhf 1.83.0.2+b2 [3816 B] Get: 93 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libbtf2 armhf 1:7.7.0+dfsg-2 [24.2 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libcamd3 armhf 1:7.7.0+dfsg-2 [37.6 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libccolamd3 armhf 1:7.7.0+dfsg-2 [39.6 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libcolamd3 armhf 1:7.7.0+dfsg-2 [32.1 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14-20240330-1 [264 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libcholmod5 armhf 1:7.7.0+dfsg-2 [606 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 106 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.61.0-1+b1 [64.1 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-5 [199 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.7.1-5 [385 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.7.1-5 [499 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libcxsparse4 armhf 1:7.7.0+dfsg-2 [79.0 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libgslcblas0 armhf 2.7.1+dfsg-6+b1 [79.6 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libgsl27 armhf 2.7.1+dfsg-6+b1 [767 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libgsl-dev armhf 2.7.1+dfsg-6+b1 [975 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1.1+b1 [1598 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf libklu2 armhf 1:7.7.0+dfsg-2 [82.0 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf liblapack-dev armhf 3.12.0-3 [1903 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libldl3 armhf 1:7.7.0+dfsg-2 [22.8 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libsuitesparse-mongoose3 armhf 1:7.7.0+dfsg-2 [46.1 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libumfpack6 armhf 1:7.7.0+dfsg-2 [267 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf librbio4 armhf 1:7.7.0+dfsg-2 [39.2 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf libspqr4 armhf 1:7.7.0+dfsg-2 [128 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libspex3 armhf 1:7.7.0+dfsg-2 [55.5 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libparu0 armhf 1:7.7.0+dfsg-2 [62.0 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libsuitesparse-dev armhf 1:7.7.0+dfsg-2 [1438 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf liblpsolve55-dev armhf 5.5.2.5-2+b1 [349 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libmysql++3t64 armhf 3.2.5-2.3 [143 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libmysql++-dev armhf 3.2.5-2.3 [145 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libncurses-dev armhf 6.5-2 [309 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libsqlite3-dev armhf 3.45.3-1 [988 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.19.2-1+b1 [614 kB] Fetched 74.9 MB in 1s (50.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19445 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19761 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../5-libreadline8t64_8.2-4_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20753 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_armhf.deb ... Unpacking python3 (3.11.8-1) ... 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_armhf.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%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_armhf.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.1-1_armhf.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../011-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../013-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../014-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../015-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../016-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../017-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../018-ruby-sdbm_1.0.0-5+b4_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../019-libbsd0_0.12.2-1_armhf.deb ... Unpacking libbsd0:armhf (0.12.2-1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../020-libedit2_3.1-20240517-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20240517-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../021-libncurses6_6.5-2_armhf.deb ... Unpacking libncurses6:armhf (6.5-2) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../022-libyaml-0-2_0.2.5-1+b1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:armhf. Preparing to unpack .../023-libruby3.1t64_3.1.2-8.3_armhf.deb ... Unpacking libruby3.1t64:armhf (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../024-ruby3.1_3.1.2-8.3_armhf.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../025-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../026-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../027-ruby_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../028-ruby-asciidoctor_2.0.20-1_all.deb ... Unpacking ruby-asciidoctor (2.0.20-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../029-asciidoctor_2.0.20-1_all.deb ... Unpacking asciidoctor (2.0.20-1) ... Selecting previously unselected package m4. Preparing to unpack .../030-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../031-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../032-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../033-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../034-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package chrpath. Preparing to unpack .../035-chrpath_0.16-2+b1_armhf.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../036-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../037-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../038-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../039-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../040-libparams-util-perl_1.102-3_armhf.deb ... Unpacking libparams-util-perl (1.102-3) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../041-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../042-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../043-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libsub-prototype-perl. Preparing to unpack .../044-libsub-prototype-perl_0.03-2+b2_armhf.deb ... Unpacking libsub-prototype-perl (0.03-2+b2) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../045-libsub-override-perl_0.11-1_all.deb ... Unpacking libsub-override-perl (0.11-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../048-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... 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Unpacking libsqlite3-dev:armhf (3.45.3-1) ... Selecting previously unselected package samtools. Preparing to unpack .../126-samtools_1.19.2-1+b1_armhf.deb ... Unpacking samtools (1.19.2-1+b1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (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 libkeyutils1:armhf (1.6.3-3) ... Setting up libboost1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up libgslcblas0:armhf (2.7.1+dfsg-6+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1+b1) ... Setting up libboost-regex1.83.0:armhf (1.83.0-2.1+b1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.61.0-1+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:armhf (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.1-1) ... Setting up libldl3:armhf (1:7.7.0+dfsg-2) ... Setting up file (1:5.45-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat May 25 12:00:17 UTC 2024. Universal Time is now: Sat May 25 12:00:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:10.11.8-1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libboost-serialization1.83.0:armhf (1.83.0-2.1+b1) ... Setting up libbtf2:armhf (1:7.7.0+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libsqlite3-dev:armhf (3.45.3-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:armhf (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libssl-dev:armhf (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up icu-devtools (72.1-4+b1) ... Setting up libmariadb3:armhf (1:10.11.8-1) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-5) ... Setting up libparams-util-perl (1.102-3) ... Setting up libgfortran5:armhf (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsuitesparseconfig7:armhf (1:7.7.0+dfsg-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libssh2-1t64:armhf (1.11.0-5) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:armhf (72.1-4+b1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libbz2-dev:armhf (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 libmysql++3t64:armhf (3.2.5-2.3) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libncurses-dev:armhf (6.5-2) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libamd3:armhf (1:7.7.0+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:armhf (1:7.7.0+dfsg-2) ... Setting up libspex3:armhf (1:7.7.0+dfsg-2) ... Setting up libsuitesparse-mongoose3:armhf (1:7.7.0+dfsg-2) ... Setting up libedit2:armhf (3.1-20240517-1) ... Setting up libcxsparse4:armhf (1:7.7.0+dfsg-2) ... Setting up libboost-serialization1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up libcamd3:armhf (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:armhf (1:7.7.0+dfsg-2) ... Setting up libbamtools-dev:armhf (2.5.2+dfsg-5) ... Setting up liblapack-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libboost-regex1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up libboost-serialization-dev:armhf (1.83.0.2+b2) ... Setting up libccolamd3:armhf (1:7.7.0+dfsg-2) ... Setting up libmariadb-dev (1:10.11.8-1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up groff-base (1.23.0-4) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libmariadb-dev-compat (1:10.11.8-1) ... Setting up libcholmod5:armhf (1:7.7.0+dfsg-2) ... Setting up libspqr4:armhf (1:7.7.0+dfsg-2) ... Setting up libboost-iostreams1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-5) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up rubygems-integration (1.18) ... Setting up libboost-iostreams-dev:armhf (1.83.0.2+b2) ... Setting up libcurl4-gnutls-dev:armhf (8.7.1-5) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libklu2:armhf (1:7.7.0+dfsg-2) ... Setting up libumfpack6:armhf (1:7.7.0+dfsg-2) ... Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libsub-override-perl (0.11-1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up default-libmysqlclient-dev:armhf (1.1.0+b1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhts-dev:armhf (1.19+ds-1.1+b1) ... Setting up libparu0:armhf (1:7.7.0+dfsg-2) ... Setting up python3 (3.11.8-1) ... Setting up samtools (1.19.2-1+b1) ... Setting up libmysql++-dev:armhf (3.2.5-2.3) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libsuitesparse-dev:armhf (1:7.7.0+dfsg-2) ... Setting up debhelper (13.15.3) ... Setting up liblpsolve55-dev (5.5.2.5-2+b1) ... Setting up libruby:armhf (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... 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:armhf (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:armhf (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Processing triggers for libc-bin (2.38-11) ... 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 armhf 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c aln2wig.c cc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/usr/include/bamtools -c bam2hints.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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:672:14: note: in a call to allocation function 'malloc' declared here 672 | 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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c filterBam.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/initOptions.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -c gene.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -c genome.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -c sqliteDB.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c joingenes.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c jg_transcript.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c jg_ios.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 -j3 "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; g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc 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. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' cd compileSpliceCands; make; 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' cd filterBam; make; 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) make[5]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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" In file included from /usr/include/c++/13/map:62, from src/Compute_UTRs.hpp:14, from src/Compute_UTRs.cpp:8: /usr/include/c++/13/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:1129:41: warning: 'idx_former_scaff' may be used uninitialized [-Wmaybe-uninitialized] 1129 | 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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" In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39, from ../include/properties.hh:14, from properties.cc:8: /usr/include/c++/13/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]', inlined from 'bool nlohmann::detail::json_sax_dom_callback_parser::key(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5599:76: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5423:41: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5397:41: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::nullptr_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = double&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::number_float(number_float_t, const string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5379:21, inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10382:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::nullptr_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = std::nullptr_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::null() [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5355:21, inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10401:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = long long int&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::number_integer(number_integer_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5367:21, inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10419:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = std::__cxx11::basic_string&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::string(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5385:21, inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10428:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = long long unsigned int&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, inlined from 'bool nlohmann::detail::json_sax_dom_parser::number_unsigned(number_unsigned_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5373:21, inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10437:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc Finished building: src/Genomic_Data.cpp Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: g++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: src/Splice_Sites.cpp Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: g++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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" In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PP::Column; _Alloc = std::allocator]', inlined from 'PP::Block::Block(PP::DistanceType, const std::vector >&, std::string)' at pp_profile.cc:206:30: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)' at pp_profile.cc:365:39: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)' at pp_profile.cc:376:39: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)' at pp_profile.cc:380:24: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)' at pp_profile.cc:388:30: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)' at pp_profile.cc:390:22: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ Finished building: src/Supporting_Methods.cpp Building file: src/Test.cpp Invoking: GCC C++ Compiler: g++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = LLDouble; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:257:30: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:260:27: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:263:34: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'bool PP::Block::initThresholds()' at pp_profile.cc:264:27: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Finished building: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = PP::Block; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void PP::Profile::parse_stream(std::istream&)' at pp_profile.cc:682:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39: /usr/include/c++/13/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair&}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2503:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2503 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h:2503:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1139:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:88:18: /usr/include/c++/13/bits/stl_tree.h:1239:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1239 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function 'std::__enable_if_t, _Pair>::value, typename std::_Rb_tree<_Key, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair) const' at ../include/vitmatrix.hh:317:27, inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19, inlined from 'void ViterbiSubmapType::push_back(SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:326:12, inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:114:23: /usr/include/c++/13/bits/stl_map.h:927:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 927 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 928 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::__enable_if_t, _Pair>::value, typename std::_Rb_tree<_Key, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair) const' at ../include/vitmatrix.hh:317:27, inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19, inlined from 'void ViterbiSubmapType::push_back(SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:326:12, inlined from 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)' at pp_scoring.cc:122:22: /usr/include/c++/13/bits/stl_map.h:927:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 927 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 928 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2521:19: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2521 | _M_erase_aux(__p.first, __p.second); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17, inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:183:28: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17, inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:196:28: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17, inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:220:31: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17, inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:234:27: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::eraseAndDecCounts(iterator) const' at ../include/vitmatrix.hh:418:17, inlined from 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)' at pp_scoring.cc:247:31: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PP::BonusProbEntry; _Alloc = std::allocator]', inlined from 'void PP::BonusProbType::push_back(int, const Double&)' at ../include/pp_scoring.hh:68:17, inlined from 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)' at pp_scoring.cc:266:19: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::__enable_if_t, _Pair>::value, typename std::_Rb_tree<_Key, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair) const' at ../include/vitmatrix.hh:317:27, inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19, inlined from 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)' at pp_scoring.cc:310:16: /usr/include/c++/13/bits/stl_map.h:927:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 927 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 928 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1139:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, inlined from 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)' at pp_scoring.cc:549:21: /usr/include/c++/13/bits/stl_tree.h:1239:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1239 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52, inlined from 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)' at pp_scoring.cc:806:18, inlined from 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)' at pp_scoring.cc:791:6: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52, inlined from 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)' at pp_scoring.cc:386:22: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from src/Genomic_Data.hpp:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1139:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, inlined from 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)' at pp_scoring.cc:499:19: /usr/include/c++/13/bits/stl_tree.h:1239:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1239 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:428:52, inlined from 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)' at pp_scoring.cc:524:26: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void boost::assign_detail::call_push_back::operator()(T&&) [with T = double; C = std::vector >]' at /usr/include/boost/assign/list_inserter.hpp:91:25, inlined from 'void boost::assign::list_inserter::insert(single_arg_type, T&&) [with T = double; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:417:20, inlined from 'boost::assign::list_inserter& boost::assign::list_inserter::operator()(Ts&& ...) [with Ts = {double}; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:409:19, inlined from 'boost::assign::list_inserter >, V> boost::assign::operator+=(std::vector<_Tp, _Alloc>&, V2&&) [with V = double; A = std::allocator; V2 = double]' at /usr/include/boost/assign/std/vector.hpp:42:30, inlined from 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map&)' at src/UTRs.cpp:382:7: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from statemodel.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Ancestor; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void StateModel::initPredecessors(Matrix&, int)' at statemodel.cc:45:24: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc Finished building: src/UTRs.cpp Building file: src/main.cpp Invoking: GCC C++ Compiler: g++ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from ../include/types.hh:38, from types.cc:8: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'Double quantile(const std::vector&, float)' at types.cc:513:12: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'Double quantile(const std::vector&, float)' at types.cc:513:12: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Constant::init()' at types.cc:356:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Constant::init()' at types.cc:363:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Constant::init()' at types.cc:370:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from ../include/motif.hh:13, from ../include/gene.hh:12, from gene.cc:8: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from motif.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'Double Motif::getProbThreshold(double, int)' at motif.cc:452:28: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/list:66, from ../include/vitmatrix.hh:17, from ../include/pp_scoring.hh:16, from ../include/gene.hh:13: /usr/include/c++/13/bits/list.tcc: In function 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator; _Tp = PP::Match; _Alloc = std::allocator]': /usr/include/c++/13/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 308 | list<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3432:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3441:14: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void examineBaseCountOfGeneSeq(AnnoSequence*)' at gene.cc:3441:14: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]', inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]' at /usr/include/c++/13/bits/list.tcc:267:5, inlined from 'static StatePath* StatePath::condenseStatePath(StatePath*)' at gene.cc:995:37: /usr/include/c++/13/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]', inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]' at /usr/include/c++/13/bits/list.tcc:267:5, inlined from 'Gene::Gene(const Gene&)' at gene.cc:1391:28: /usr/include/c++/13/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/statemodel.hh:13, from ../include/intronmodel.hh:11, from intronmodel.cc:8: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static Double IntronModel::aSSProb(int, bool)' at intronmodel.cc:1184:12: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static Double IntronModel::aSSProb(int, bool)' at intronmodel.cc:1186:12: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static Double IntronModel::dSSProb(int, bool)' at intronmodel.cc:1241:16: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = LLDouble; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static Double IntronModel::dSSProb(int, bool)' at intronmodel.cc:1243:16: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from extrinsicinfo.cc:10: /usr/include/c++/13/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]': /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::less, std::allocator >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../include/types.hh:38: /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = _Rb_tree_const_iterator; _InputIterator2 = _Rb_tree_const_iterator; _OutputIterator = insert_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5383 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5383:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2518:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2524:17: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2537:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2558:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2564:17: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2576:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2596:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2602:17: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2614:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2642:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2648:17: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2660:20: /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 5448 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:5448:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from ../include/types.hh:38, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'static std::vector CRF::capOutliers(std::vector)' at merkmal.cc:841:11: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'static std::vector CRF::capOutliers(std::vector)' at merkmal.cc:841:11: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector, FeatureCollection&)' at merkmal.cc:396:14: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from ../include/types.hh:39: /usr/include/c++/13/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair&}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function 'std::__enable_if_t, _Pair>::value, typename std::_Rb_tree<_Key, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const_iterator, _Pair&&) [with _Pair = std::pair&; _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, std::pair) const' at ../include/vitmatrix.hh:317:27, inlined from 'ViterbiSubmapType::iterator ViterbiSubmapType::insert(iterator, SubstateId, const Double&, ViterbiSubmapType*) const' at ../include/vitmatrix.hh:322:19, inlined from 'void ViterbiSubmapType::merge(ViterbiSubmapType&, Double)' at vitmatrix.cc:73:9: /usr/include/c++/13/bits/stl_map.h:927:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 927 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 928 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::registerPredecessors()' at vitmatrix.cc:131:35: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'short int& ViterbiSubmapType::succCount(SubstateId)' at ../include/vitmatrix.hh:335:27, inlined from 'void ViterbiSubmapType::registerPredecessors()' at vitmatrix.cc:148:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2503:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2503 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h:2503:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1139:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, inlined from 'void ViterbiSubmapType::useMaximum(Double&)' at vitmatrix.cc:164:10: /usr/include/c++/13/bits/stl_tree.h:1239:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1239 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1139:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, inlined from 'void ViterbiSubmapType::useMaximum(Double&)' at vitmatrix.cc:166:7: /usr/include/c++/13/bits/stl_tree.h:1239:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1239 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::size_type std::map<_Key, _Tp, _Compare, _Alloc>::erase(const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:1119:26, inlined from 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)' at vitmatrix.cc:103:18: /usr/include/c++/13/bits/stl_tree.h:2521:19: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2521 | _M_erase_aux(__p.first, __p.second); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ViterbiEntryType; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void ViterbiColumnType::addState(int, signed char)' at vitmatrix.cc:289:14: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ViterbiSubmapType; _Alloc = std::allocator]', inlined from 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)' at vitmatrix.cc:234:23: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void BinnedMMGroup::trainBins(int)' at merkmal.cc:111:14: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void BinnedMMGroup::trainBins(int)' at merkmal.cc:111:14: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from ../include/gene.hh:12, from ../include/mea.hh:11, from mea.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)' at ../include/graph.hh:344:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/ncmodel.hh:11, from ncmodel.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void NcModel::computeLengthDistributions()' at ncmodel.cc:142:25: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from ../include/gene.hh:12, from ../include/randseqaccess.hh:12, from randseqaccess.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = hints; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void mysqlpp::Query::storein_sequence(Sequence&, const mysqlpp::SQLTypeAdapter&) [with Sequence = std::vector]' at /usr/include/mysql++/query.h:763:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from contTimeMC.cc:10: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Evo::setBranchLengths(std::vector, int)' at contTimeMC.cc:52:9: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Evo::setBranchLengths(std::vector, int)' at contTimeMC.cc:52:9: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from contTimeMC.cc:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void ExonEvo::addBranchLength(double)' at contTimeMC.cc:387:17: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from ../include/codonevo.hh:11, from codonevo.cc:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void CodonEvo::setPrior(double)' at codonevo.cc:64:22: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:42:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:43:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:45:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CodonEvo::setOmegas(int)' at codonevo.cc:48:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from geneMSA.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'Parsimony::Parsimony()' at ../include/contTimeMC.hh:185:23, inlined from 'double CodonEvo::estOmegaOnSeqTuple(std::vector >&, PhyloTree*, int&)' at codonevo.cc:553:15: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void CodonEvo::setAAPostProbs()' at codonevo.cc:92:17: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void GeneMSA::calcConsScore(std::__cxx11::list&, const std::vector&, std::string)' at geneMSA.cc:1705:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void cumValues::addLogliks(std::vector*)' at ../include/geneMSA.hh:41:21, inlined from 'void GeneMSA::computeOmegasEff(std::__cxx11::list&, const std::vector&, PhyloTree*, std::ofstream*)' at geneMSA.cc:1560:17: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/phylotree.hh:13, from phylotree.cc:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::pruningAlgor(std::vector&, Evo*, int)' at phylotree.cc:249:23: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::pruningAlgor(std::vector&, Evo*, int)' at phylotree.cc:252:23: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::pruningAlgor(std::vector&, Evo*, int)' at phylotree.cc:258:26: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::MAP(std::vector&, std::vector&, Evo*, bool)' at phylotree.cc:402:26: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::MAP(std::vector&, std::vector&, Evo*, bool)' at phylotree.cc:415:26: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'int PhyloTree::fitch(std::vector&, int)' at phylotree.cc:543:26: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'int PhyloTree::fitch(std::vector&, int)' at phylotree.cc:550:26: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void PhyloTree::getBranchLengths(std::vector&) const' at phylotree.cc:320:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from ../include/compgenepred.hh:12, from compgenepred.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)' at ../include/graph.hh:344:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:282:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:284:41: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:288:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:295:26: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/exoncand.hh:13, from ../include/orthoexon.hh:11, from orthoexon.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void OrthoExon::setOmega(std::vector*, CodonEvo*, bool)' at orthoexon.cc:168:25: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'OrthoExon::OrthoExon(int_fast64_t, size_t)' at orthoexon.cc:21:19: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/intronmodel.hh:11, from introntrain.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47, inlined from 'void IntronModel::makeDSSProbs()' at introntrain.cc:583:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/exonmodel.hh:11, from exontrain.cc:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47, inlined from 'void IntronModel::buildProbabilities(const AnnoSequence*)' at introntrain.cc:415:28: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47, inlined from 'void ExonModel::buildProbabilities()' at exontrain.cc:130:27: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47, inlined from 'void ExonModel::buildProbabilities()' at exontrain.cc:135:27: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc cp -f prepareAlign ../bin/ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from ../include/properties.hh:14, from ../include/pp_simscore.hh:21, from pp_simscore.cc:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cp -f load2db ../bin/ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void SS::SimilarityScore::printAlignment()' at pp_simscore.cc:723:56: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp -f getSeq ../bin/ 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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 cp -f pp_simScore ../bin/ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 cp -f load2sqlitedb ../bin/ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 In file included from /usr/include/c++/13/vector:72, from ../include/types.hh:36, from etraining.cc:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void CRF::compareWeights(Parameters*, std::vector&, std::vector&, int) [with U = double; V = double]' at ../include/merkmal.hh:277:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp -f fastBlockSearch ../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 -j3 test make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' mkdir -p bin cd src && make mkdir -p bin 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. 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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags 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[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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[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' If you run make test on a non-AMD64 architecture or a non-Linux system (like macOS), most tests will run without the --compare option! cd tests/short && ./execute_test.py 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 1497.367s 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 0.059s 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 0.138s 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 2.280s 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 dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-4_armhf.deb'. dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-4_all.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-4_armhf.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_armhf.buildinfo dpkg-genchanges --build=binary -O../augustus_3.5.0+dfsg-4_armhf.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/27723 and its subdirectories I: Current time: Sat May 25 00:45:22 -12 2024 I: pbuilder-time-stamp: 1716641122 Sat May 25 12:47:56 UTC 2024 I: 1st build successful. Starting 2nd build on remote node cbxi4a-armhf-rb.debian.net. Sat May 25 12:47:56 UTC 2024 I: Preparing to do remote build '2' on cbxi4a-armhf-rb.debian.net. Sat May 25 14:52:24 UTC 2024 I: Deleting $TMPDIR on cbxi4a-armhf-rb.debian.net. Sat May 25 14:52:27 UTC 2024 I: augustus_3.5.0+dfsg-4_armhf.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 armhf 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 1a59786a9dfae9b841c295993702130455721ce6 35104812 augustus-dbgsym_3.5.0+dfsg-4_armhf.deb f4e24b51f985e464517b40767a7ac40445b5b588 23671260 augustus-doc_3.5.0+dfsg-4_all.deb 61193e95b0004679ddfe64142f472ee912b62d77 9300 augustus_3.5.0+dfsg-4_armhf.buildinfo c7da3f1486dda1a2699262a45a073bd1fed2039c 1720292 augustus_3.5.0+dfsg-4_armhf.deb Checksums-Sha256: d715a3c382ecdc35431d3b0343c65842b93dea90a22dc401c726eff32638550f 20263840 augustus-data_3.5.0+dfsg-4_all.deb 75eb9433e9c9feac6cee5918f466a7e0a1464ff60c6392ae38f622017b8597ba 35104812 augustus-dbgsym_3.5.0+dfsg-4_armhf.deb cb27e8da343bce5677f52b5ea9208923a02158be71353b6aff6e50165cf616fa 23671260 augustus-doc_3.5.0+dfsg-4_all.deb 326cd652413e4afb375fb2e19c9c47c8f561bf9f0a75f884be6c96ac7db79da7 9300 augustus_3.5.0+dfsg-4_armhf.buildinfo dcda47ce8da2df13b204bfb4792910d557b33b0181aa362034733da12fddc3ee 1720292 augustus_3.5.0+dfsg-4_armhf.deb Files: f7fdf3f6365c1100b62954f7c3b2a6ef 20263840 science optional augustus-data_3.5.0+dfsg-4_all.deb 4e56de804a4dad5883a1b9f53c7eb0ca 35104812 debug optional augustus-dbgsym_3.5.0+dfsg-4_armhf.deb b1983e0b0ce0d1b8e9fabcb118c034ea 23671260 doc optional augustus-doc_3.5.0+dfsg-4_all.deb 7ce2444578e5fddd3c52d523fb285b15 9300 science optional augustus_3.5.0+dfsg-4_armhf.buildinfo c4757d70cfee0241398ddd4a594e11ba 1720292 science optional augustus_3.5.0+dfsg-4_armhf.deb Sat May 25 14:52:28 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_7-2929.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OpohdMCj/augustus_3.5.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OpohdMCj/augustus_3.5.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OpohdMCj/augustus_3.5.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OpohdMCj/b1/augustus_3.5.0+dfsg-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.OpohdMCj/b2/augustus_3.5.0+dfsg-4_armhf.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: 1.357s) 1.357s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.951s) 0.951s 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: 1.730s CPU time consumed: 1.728s Sat May 25 14:52:30 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Sat May 25 14:52:30 UTC 2024 I: augustus from trixie built successfully and reproducibly on armhf. Sat May 25 14:52:32 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 25 14:52:32 UTC 2024 I: Submitting 12K b1/augustus_3.5.0+dfsg-4_armhf.buildinfo.asc Sat May 25 14:52:33 UTC 2024 I: Submitting 12K b2/augustus_3.5.0+dfsg-4_armhf.buildinfo.asc Sat May 25 14:52:36 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 25 14:52:36 UTC 2024 I: Done submitting .buildinfo files. Sat May 25 14:52:36 UTC 2024 I: Removing signed augustus_3.5.0+dfsg-4_armhf.buildinfo.asc files: removed './b1/augustus_3.5.0+dfsg-4_armhf.buildinfo.asc' removed './b2/augustus_3.5.0+dfsg-4_armhf.buildinfo.asc'