Diff of the two buildlogs: -- --- b1/build.log 2024-12-08 10:08:47.644302792 +0000 +++ b2/build.log 2024-12-08 10:12:40.105747734 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 7 22:06:25 -12 2024 -I: pbuilder-time-stamp: 1733652385 +I: Current time: Sun Jan 11 06:31:50 +14 2026 +I: pbuilder-time-stamp: 1768062710 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/1415288/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2178715/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 Jan 10 16:31 /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/2178715/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2178715/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' + 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(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 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='bf7fb3384f5844eabaa54e39be2f748c' - 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='1415288' - PS1='# ' - PS2='> ' + INVOCATION_ID=076a4fe21b974bf3b5e526b3114d668c + 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=2178715 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.Y4i8bg0y/pbuilderrc_Ji7b --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.Y4i8bg0y/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-4.dsc' - SUDO_GID='109' - 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.Y4i8bg0y/pbuilderrc_HUvw --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.Y4i8bg0y/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-4.dsc' + SUDO_GID=109 + 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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1415288/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2178715/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -244,7 +276,7 @@ Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 103 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] -Fetched 66.0 MB in 1s (102 MB/s) +Fetched 66.0 MB in 1s (118 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 20083 files and directories currently installed.) @@ -675,7 +707,11 @@ 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/2178715/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/2178715/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 @@ -708,7 +744,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (0.5s) +-- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -756,8 +792,8 @@ [ 45%] 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [ 55%] 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -767,42 +803,7 @@ 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/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.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/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( - | ^~~~~~~~~~~~~~~~~~~~ -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/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( - | ^~~~~~~~~~~~~~~~~~~~ -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/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/edge.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( | ^~~~~~~~~~~~~~~~~~~~ @@ -817,16 +818,6 @@ /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/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/edge.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 | ^~~~~~~~ @@ -856,16 +847,9 @@ 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( - | ^~~~~~~~~~~~~~~~~~~~ -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: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -889,17 +873,7 @@ 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: -/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/fasta.cpp:7: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -912,6 +886,16 @@ /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/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: +/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/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 @@ -919,12 +903,32 @@ /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/fasta.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/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/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/util.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 | ^~~~~~~~ @@ -965,20 +969,6 @@ /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/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ @@ -1000,6 +990,18 @@ /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/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( + | ^~~~~~~~~~~~~~~~~~~~ /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 | ^~~~~~~~ @@ -1009,40 +1011,55 @@ /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 - | ^~~~~~~~ +[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /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/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: 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 | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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/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_; - | ^~~~~~~~ /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/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: +/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/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 @@ -1054,23 +1071,6 @@ /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 - | ^~~~~~~~ -[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -/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/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1080,13 +1080,20 @@ /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: /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 | ^~~~~~~~ @@ -1096,12 +1103,6 @@ /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 /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] @@ -1110,6 +1111,12 @@ /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 + | ^~~~~~~~ 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_; @@ -1119,41 +1126,12 @@ /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 - | ^~~~~~~~ /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 - | ^~~~~~~~ -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 - | ^~~~~~~~ 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_; @@ -1169,8 +1147,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -1185,23 +1161,33 @@ /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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 | ^~~~~~~~ -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: +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, - 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: + 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 + | ^~~~~~~~ +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 | ^~~~~~~~ @@ -1214,26 +1200,27 @@ /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/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/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( - | ^~~~~~~~~~~~~~~~~~~~ +/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_; + | ^~~~~~~~ +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 /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, @@ -1247,11 +1234,10 @@ /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: +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 | ^~~~~~~~ @@ -1264,12 +1250,6 @@ /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 | ^~~~~~~~ @@ -1293,17 +1273,20 @@ /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/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 + | ^~~~~~~~ +[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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: /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: + 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; | ^~~~~~~~ @@ -1313,6 +1296,47 @@ /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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 + | ^~~~~~~~ +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/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( + | ^~~~~~~~~~~~~~~~~~~~ /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 | ^~~~~~~~ @@ -1322,10 +1346,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /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 /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] @@ -1334,30 +1354,28 @@ /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/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 | ^~~~~~~~ -/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/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 + | ^~~~~~~~ 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_; @@ -1376,9 +1394,10 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -1386,8 +1405,8 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -1397,7 +1416,9 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -1407,36 +1428,33 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] +/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/test/../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/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] +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 | ^~~~~~~~ -[ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +/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 | ^~~~~~~~ -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 | ^~~~~~~~ @@ -1449,28 +1467,35 @@ /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_; + | ^~~~~~~~ /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 /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 - | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ 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 - | ^~~~~~~~ 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 @@ -1498,15 +1523,13 @@ /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/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( - | ^~~~~~~~~~~~~~~~~~~~ +/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 | ^~~~~~~~ @@ -1516,6 +1539,19 @@ /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: +/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 + | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file,CMakeFiles/Sibelia.dir/link.d CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort @@ -1659,12 +1695,14 @@ 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/2178715/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2178715/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/1415288 and its subdirectories -I: Current time: Sat Dec 7 22:08:46 -12 2024 -I: pbuilder-time-stamp: 1733652526 +I: removing directory /srv/workspace/pbuilder/2178715 and its subdirectories +I: Current time: Sun Jan 11 06:35:38 +14 2026 +I: pbuilder-time-stamp: 1768062938