Diff of the two buildlogs: -- --- b1/build.log 2023-04-19 13:39:49.370908685 +0000 +++ b2/build.log 2023-04-19 13:45:31.091740316 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 19 01:33:24 -12 2023 -I: pbuilder-time-stamp: 1681911204 +I: Current time: Wed May 22 10:02:57 +14 2024 +I: pbuilder-time-stamp: 1716321777 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Apr 13 20:37:29 2020 -12 +gpgv: Signature made Tue Apr 14 22:37:29 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key @@ -31,52 +31,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7766/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22459/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-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 May 22 10:03 /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/22459/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22459/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='7766' - PS1='# ' - PS2='> ' + 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=22459 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.z78KlMSv/pbuilderrc_VQ0d --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z78KlMSv/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.z78KlMSv/pbuilderrc_ZjOM --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z78KlMSv/b2 --logfile b2/build.log --extrapackages usrmerge sibelia_3.0.7+dfsg-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 18 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/7766/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 22 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/22459/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -187,7 +219,7 @@ Get: 61 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libseqan2-dev all 2.4.0+dfsg-15 [1215 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] -Fetched 48.1 MB in 3s (14.3 MB/s) +Fetched 48.1 MB in 3s (15.5 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 ... 19616 files and directories currently installed.) @@ -453,8 +485,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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-3_source.changes +I: user script /srv/workspace/pbuilder/22459/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/22459/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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-3_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -504,40 +545,40 @@ -- Build files have been written to: /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu dh_auto_build -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[1]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan cd /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' -[ 10%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o -[ 10%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -[ 15%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o +[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o +[ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o +[ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/sibelia.cpp +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/postprocessor.cpp /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/indexedsequence.cpp.o -MF CMakeFiles/Sibelia.dir/indexedsequence.cpp.o.d -o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -c /build/sibelia-3.0.7+dfsg/src/indexedsequence.cpp /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/util.cpp -[ 20%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/postprocessor.cpp -[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/outputgenerator.cpp -[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/blockfinder.cpp -[ 35%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -[ 40%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/blockinstance.cpp +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -545,15 +586,7 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/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.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -561,7 +594,8 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -576,11 +610,18 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -592,25 +633,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/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/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++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/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/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++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -622,6 +662,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/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 | ^~~~~~~~ @@ -630,9 +676,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/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/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++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -644,6 +699,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/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++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/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 | ^~~~~~~~ @@ -658,20 +727,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/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_; | ^~~~~~~~ @@ -680,24 +743,23 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/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 + | ^~~~~~~~ /build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -/build/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/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++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -722,6 +784,7 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/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_; | ^~~~~~~~ @@ -736,28 +799,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -/build/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++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/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_; @@ -791,12 +832,28 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/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.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/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.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/serialization.cpp /build/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] @@ -809,37 +866,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/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 /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:14: -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/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/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 | ^~~~~~~~ @@ -859,6 +885,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:14: +/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/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 | ^~~~~~~~ @@ -885,6 +926,21 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: +/build/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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/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/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 | ^~~~~~~~ @@ -893,8 +949,7 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/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 | ^~~~~~~~ @@ -907,36 +962,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: -/build/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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: -/build/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++/12/memory:76, - from /build/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ -/build/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++/12/bits/unique_ptr.h:64:28: note: declared here - 64 | template class auto_ptr; - | ^~~~~~~~ /build/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 | ^~~~~~~~ @@ -945,7 +977,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/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 | ^~~~~~~~ @@ -958,14 +991,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/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( - | ^~~~~~~~~~~~~~~~~~~~ /build/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 | ^~~~~~~~ @@ -1003,13 +1028,51 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/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++/12/memory:76, + from /build/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +/build/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++/12/bits/unique_ptr.h:64:28: note: declared here + 64 | template class auto_ptr; + | ^~~~~~~~ +/build/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++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/12/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/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/synteny.cpp +[ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/fasta.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/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.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/platform.cpp /build/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 | ^~~~~~~~ @@ -1047,32 +1110,6 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -[ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/synteny.cpp -/build/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++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp -[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/platform.cpp -[ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/stranditerator.cpp -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp /build/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 | ^~~~~~~~ @@ -1110,15 +1147,8 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/resource.cpp -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/platform.h:10, - from /build/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( - | ^~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/stranditerator.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, @@ -1128,22 +1158,15 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/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.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/platform.h:10, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp +[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/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/sibelia-3.0.7+dfsg/src/resource.cpp /build/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 | ^~~~~~~~ @@ -1167,6 +1190,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/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/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 | ^~~~~~~~ @@ -1182,12 +1213,29 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ /build/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/resource.h:6, + from /build/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/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 | ^~~~~~~~ @@ -1209,6 +1257,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/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++/12/string:45, + from /build/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/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_; | ^~~~~~~~ @@ -1223,58 +1279,43 @@ /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/resource.h:6, - from /build/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/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++/12/string:45, - from /build/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/12/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/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic 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 -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[1]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt binnengegaan dh_auto_test --no-parallel -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[1]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan cd /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'CMakeFiles/Sibelia.dir/build'. +make[3]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' -make[2]: Nothing to be done for 'preinstall'. -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt binnengegaan +make[2]: Er hoeft niets gedaan te worden voor 'preinstall'. +make[2]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" @@ -1334,21 +1375,21 @@ -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' +make[1]: Map '/build/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' wordt verlaten debian/rules override_dh_install -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt binnengegaan dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt verlaten dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt binnengegaan dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Map '/build/sibelia-3.0.7+dfsg' wordt verlaten dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src @@ -1367,9 +1408,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-3_arm64.deb'. -dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-3_all.deb'. -dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-3_arm64.deb'. +dpkg-deb: pakket 'sibelia-dbgsym' wordt gebouwd in '../sibelia-dbgsym_3.0.7+dfsg-3_arm64.deb'. +dpkg-deb: pakket 'sibelia' wordt gebouwd in '../sibelia_3.0.7+dfsg-3_arm64.deb'. +dpkg-deb: pakket 'sibelia-examples' wordt gebouwd in '../sibelia-examples_3.0.7+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1377,12 +1418,14 @@ 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/22459/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22459/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/7766 and its subdirectories -I: Current time: Wed Apr 19 01:39:48 -12 2023 -I: pbuilder-time-stamp: 1681911588 +I: removing directory /srv/workspace/pbuilder/22459 and its subdirectories +I: Current time: Wed May 22 10:08:30 +14 2024 +I: pbuilder-time-stamp: 1716322110