Diff of the two buildlogs: -- --- b1/build.log 2024-11-25 23:28:26.106842201 +0000 +++ b2/build.log 2024-11-25 23:35:34.671518636 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 25 11:26:11 -12 2024 -I: pbuilder-time-stamp: 1732577171 +I: Current time: Mon Dec 29 19:51:53 +14 2025 +I: pbuilder-time-stamp: 1766987513 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -33,54 +33,86 @@ dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/56080/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/81265/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 29 05:53 /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/81265/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/81265/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='i386' + 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]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='4f2f05aadb3f463f91b93c3fe1eee99f' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='56080' - PS1='# ' - PS2='> ' + INVOCATION_ID=981c0eb7828647b8af47db404b255a75 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=81265 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.MSAqqDrz/pbuilderrc_Nu42 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MSAqqDrz/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.MSAqqDrz/pbuilderrc_4Mhz --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MSAqqDrz/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/56080/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/81265/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -247,7 +279,7 @@ Get: 102 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.20+ds-2 [1693 kB] Get: 103 http://deb.debian.org/debian experimental/main i386 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] -Fetched 70.7 MB in 1s (49.4 MB/s) +Fetched 70.7 MB in 2s (45.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19951 files and directories currently installed.) @@ -678,7 +710,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/sibelia-3.0.7+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 > ../sibelia_3.0.7+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/81265/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/81265/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sibelia-3.0.7+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 > ../sibelia_3.0.7+dfsg-4_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-4 dpkg-buildpackage: info: source distribution experimental @@ -711,7 +747,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (0.5s) +-- Configuring done (1.4s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -728,7 +764,7 @@ -- Build files have been written to: /build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu dh_auto_build -O--sourcedirectory=src - cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -740,27 +776,43 @@ make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' -[ 5%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o -[ 15%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -[ 15%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o -[ 20%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o -[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -[ 30%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o +[ 5%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp +[ 10%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp +[ 15%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp +[ 20%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o +[ 30%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp -[ 35%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -[ 40%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o -[ 45%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o +[ 35%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp +[ 40%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o +[ 45%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d 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/build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp +[ 55%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o +[ 65%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o +[ 65%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp +[ 70%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp +[ 75%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp +[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp +[ 85%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp +[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o +[ 95%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, @@ -768,9 +820,16 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -780,7 +839,7 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -790,9 +849,8 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -801,7 +859,8 @@ from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -809,9 +868,20 @@ from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -829,11 +899,9 @@ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -851,9 +919,21 @@ from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -866,6 +946,47 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -882,6 +1003,50 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] @@ -896,6 +1061,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ @@ -925,6 +1107,7 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -942,15 +1125,6 @@ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: @@ -962,14 +1136,6 @@ /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -988,15 +1154,63 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1018,34 +1232,12 @@ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] @@ -1054,12 +1246,17 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here @@ -1068,12 +1265,37 @@ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1099,7 +1321,12 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -1114,13 +1341,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -1150,79 +1370,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -[ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp -[ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp -[ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp -[ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp -[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/tclap/SwitchArg.h:29, - from /usr/include/tclap/CmdLine.h:27, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator - | ^~~~~~~~ + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1235,30 +1388,6 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /usr/include/seqan/basic/test_system.h:53, - from /usr/include/seqan/basic.h:65, - from /usr/include/seqan/align.h:55, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1268,69 +1397,19 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /usr/include/seqan/align.h:53, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1354,24 +1433,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -1396,59 +1457,13 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1457,11 +1472,15 @@ | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: + from /usr/include/tclap/SwitchArg.h:29, + from /usr/include/tclap/CmdLine.h:27, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1474,51 +1493,68 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /usr/include/seqan/basic/test_system.h:53, + from /usr/include/seqan/basic.h:65, + from /usr/include/seqan/align.h:55, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /usr/include/seqan/align.h:53, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp: In function ‘void __static_initialization_and_destruction_0()’: /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:7108:1: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without 7108 | } @@ -1539,7 +1575,7 @@ dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src - cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j21 install DESTDIR=/build/reproducible-path/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -1573,51 +1609,51 @@ -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/C-SIBELIA.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/LICENSE.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia --- Installing: 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/build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta +-- Installing: 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/build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils --- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py +-- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install @@ -1652,9 +1688,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_i386.deb'. dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-4_i386.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-4_all.deb'. +dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1662,12 +1698,14 @@ 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/81265/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/81265/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/56080 and its subdirectories -I: Current time: Mon Nov 25 11:28:25 -12 2024 -I: pbuilder-time-stamp: 1732577305 +I: removing directory /srv/workspace/pbuilder/81265 and its subdirectories +I: Current time: Mon Dec 29 19:58:33 +14 2025 +I: pbuilder-time-stamp: 1766987913