Diff of the two buildlogs: -- --- b1/build.log 2025-11-11 17:34:36.566363886 +0000 +++ b2/build.log 2025-11-11 17:51:07.623420441 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 11 05:19:17 -12 2025 -I: pbuilder-time-stamp: 1762881557 +I: Current time: Tue Dec 15 13:57:39 +14 2026 +I: pbuilder-time-stamp: 1797292659 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,53 +31,85 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/360877/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 14 23:58 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1036671/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='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='76f5258c73f44553ac4c73be27cc37ec' - 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='360877' - PS1='# ' - PS2='> ' + INVOCATION_ID=b9fb3c4d872445b78722ce5e3639cde7 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1036671 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.g2qMCi9p/pbuilderrc_0sbJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g2qMCi9p/b1 --logfile b1/build.log augustus_3.5.0+dfsg-5.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.g2qMCi9p/pbuilderrc_AtCH --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g2qMCi9p/b2 --logfile b2/build.log augustus_3.5.0+dfsg-5.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/360877/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -324,7 +356,7 @@ Get: 177 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5+20250216-2 [340 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] -Fetched 99.5 MB in 1s (118 MB/s) +Fetched 99.5 MB in 4s (22.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19968 files and directories currently installed.) @@ -907,8 +939,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Nov 11 17:20:10 UTC 2025. -Universal Time is now: Tue Nov 11 17:20:10 UTC 2025. +Local time is now: Tue Dec 15 00:00:30 UTC 2026. +Universal Time is now: Tue Dec 15 00:00:30 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:11.8.3-1) ... @@ -1080,7 +1112,11 @@ 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-5_source.changes +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/augustus-3.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../augustus_3.5.0+dfsg-5_source.changes dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.5.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -1275,30 +1311,30 @@ make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc make[4]: 'aln2wig' is up to date. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc cd bam2hints; make; +make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc -make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc cd compileSpliceCands; make; -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc cd filterBam; make; +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam' (cd src;make) +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc +make[5]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc -make[5]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -1340,11 +1376,13 @@ 150 | unsigned idx_former_scaff; | ^~~~~~~~~~~~~~~~ Finished building: src/Compute_UTRs.cpp - Building file: src/Coord_Transform.cpp + Invoking: GCC C++ Compiler: g++ +Building file: src/Genomic_Data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/Coord_Transform.o" "src/Coord_Transform.cpp" -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.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 { | ^~~~~~~~~~~~~~~ @@ -1406,37 +1444,67 @@ src/Coord_Transform.cpp:65:13: note: 'skip_end' was declared here 65 | int skip_end; //normally end position + W for this next intron | ^~~~~~~~ -Building file: src/Genomic_Data.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" Finished building: src/Coord_Transform.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc +Finished building: src/Genomic_Data.cpp + Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc +Finished building: src/Splice_Sites.cpp + Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc +In file included from ../include/properties.hh:17, + from properties.cc:8: +In member function 'nlohmann::basic_json::iterator nlohmann::basic_json::begin() [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long int; NumberUnsignedType = long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; BinaryType = std::vector]', + inlined from 'nlohmann::detail::iteration_proxy_value nlohmann::detail::iteration_proxy::begin() [with IteratorType = nlohmann::detail::iter_impl >]' at ../include/json.hpp:3943:67, + inlined from 'static void Properties::init(int, char**)' at properties.cc:304:49: +../include/json.hpp:20968:18: warning: 'SR.4720' may be used uninitialized [-Wmaybe-uninitialized] +20968 | iterator result(this); + | ^~~~~~ +../include/json.hpp: In static member function 'static void Properties::init(int, char**)': +../include/json.hpp:3943:67: note: 'SR.4720' was declared here + 3943 | return iteration_proxy_value(container.begin()); + | ~~~~~~~~~~~~~~~^~ +In member function 'nlohmann::basic_json::iterator nlohmann::basic_json::end() [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long int; NumberUnsignedType = long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; BinaryType = std::vector]', + inlined from 'nlohmann::detail::iteration_proxy_value nlohmann::detail::iteration_proxy::end() [with IteratorType = nlohmann::detail::iter_impl >]' at ../include/json.hpp:3949:65, + inlined from 'static void Properties::init(int, char**)' at properties.cc:304:49: +../include/json.hpp:21039:18: warning: 'SR.4717' may be used uninitialized [-Wmaybe-uninitialized] +21039 | iterator result(this); + | ^~~~~~ +../include/json.hpp: In static member function 'static void Properties::init(int, char**)': +../include/json.hpp:3949:65: note: 'SR.4717' was declared here + 3949 | return iteration_proxy_value(container.end()); + | ~~~~~~~~~~~~~^~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc +Finished building: src/Supporting_Methods.cpp + Building file: src/Test.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" -Finished building: src/Supporting_Methods.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc +Finished building: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" -Finished building: src/Test.cpp - -Building file: src/main.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" -Finished building: src/Splice_Sites.cpp - -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc src/UTRs.cpp:83:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 83 | binary_function { | ^~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc In file included from /usr/include/c++/15/string:51, from src/Genomic_Data.hpp:8, from src/UTRs.cpp:5: @@ -1525,47 +1593,27 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc -Finished building: src/main.cpp - -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc -Finished building: src/Genomic_Data.cpp - -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc -In file included from ../include/properties.hh:17, - from properties.cc:8: -In member function 'nlohmann::basic_json::iterator nlohmann::basic_json::begin() [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long int; NumberUnsignedType = long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; BinaryType = std::vector]', - inlined from 'nlohmann::detail::iteration_proxy_value nlohmann::detail::iteration_proxy::begin() [with IteratorType = nlohmann::detail::iter_impl >]' at ../include/json.hpp:3943:67, - inlined from 'static void Properties::init(int, char**)' at properties.cc:304:49: -../include/json.hpp:20968:18: warning: 'SR.4720' may be used uninitialized [-Wmaybe-uninitialized] -20968 | iterator result(this); - | ^~~~~~ -../include/json.hpp: In static member function 'static void Properties::init(int, char**)': -../include/json.hpp:3943:67: note: 'SR.4720' was declared here - 3943 | return iteration_proxy_value(container.begin()); - | ~~~~~~~~~~~~~~~^~ -In member function 'nlohmann::basic_json::iterator nlohmann::basic_json::end() [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long int; NumberUnsignedType = long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; BinaryType = std::vector]', - inlined from 'nlohmann::detail::iteration_proxy_value nlohmann::detail::iteration_proxy::end() [with IteratorType = nlohmann::detail::iter_impl >]' at ../include/json.hpp:3949:65, - inlined from 'static void Properties::init(int, char**)' at properties.cc:304:49: -../include/json.hpp:21039:18: warning: 'SR.4717' may be used uninitialized [-Wmaybe-uninitialized] -21039 | iterator result(this); - | ^~~~~~ -../include/json.hpp: In static member function 'static void Properties::init(int, char**)': -../include/json.hpp:3949:65: note: 'SR.4717' was declared here - 3949 | return iteration_proxy_value(container.end()); - | ~~~~~~~~~~~~~^~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc +Building file: src/main.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc +Finished building: src/main.cpp + +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc Finished building: src/UTRs.cpp Building target: utrrnaseq @@ -1579,18 +1627,6 @@ make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc @@ -1605,15 +1641,15 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++ -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 -mbranch-protection=standard -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 +cp -f prepareAlign ../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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 -cp -f prepareAlign ../bin/ cp -f load2sqlitedb ../bin/ cp -f load2db ../bin/ -cp -f pp_simScore ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 +cp -f pp_simScore ../bin/ cp -f fastBlockSearch ../bin/ cp -f getSeq ../bin/ cp -f etraining ../bin/ @@ -1622,126 +1658,7 @@ 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 -j12 test -make[1]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg' -mkdir -p bin -cd src && make -make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' -mkdir -p bin -cd auxprogs && make -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]: 'aln2wig' is up to date. -make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/aln2wig' -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags -make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/src' -cd bam2hints; make; -make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/bam2hints' -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]: 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' -(cd src;make) -make[4]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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' -(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]: 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' -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]: 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 536.456s - -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 0.035s - -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 0.061s - -OK -cd tests/short && ./execute_test.py --html filterbam -test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok -test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok -test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok -test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok -test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok -test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok -test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok -test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok -test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok -test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok -test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok -test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok -test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok -test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok -test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok -test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok -test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok -test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok -test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok -test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok -test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok -test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok -test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok -test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok -test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok - ----------------------------------------------------------------------- -Ran 25 tests in 0.716s - -OK -make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg' +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install @@ -1815,10 +1732,10 @@ dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-5_arm64.deb'. dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-5_arm64.deb'. -dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-5_all.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.5.0+dfsg-5_all.deb'. -dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-5_arm64.deb'. +dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../augustus_3.5.0+dfsg-5_arm64.buildinfo dpkg-genchanges --build=binary -O../augustus_3.5.0+dfsg-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1826,12 +1743,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1036671/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/360877 and its subdirectories -I: Current time: Tue Nov 11 05:34:26 -12 2025 -I: pbuilder-time-stamp: 1762882466 +I: removing directory /srv/workspace/pbuilder/1036671 and its subdirectories +I: Current time: Tue Dec 15 14:13:59 +14 2026 +I: pbuilder-time-stamp: 1797293639