Diff of the two buildlogs: -- --- b1/build.log 2024-09-07 19:48:20.850235865 +0000 +++ b2/build.log 2024-09-07 19:55:51.751097717 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 7 07:34:27 -12 2024 -I: pbuilder-time-stamp: 1725737667 +I: Current time: Sun Sep 8 09:49:25 +14 2024 +I: pbuilder-time-stamp: 1725738565 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying offer_help_option_for_stacks_gdb.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21347/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 Sep 7 19:49 /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/1750/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='369200d1b4554ae2be04b5b2fb5a2d3f' - 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='21347' - PS1='# ' - PS2='> ' + INVOCATION_ID=45961520350d4f5e9bb4f9e053818f9a + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=1750 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.cGr7VG6O/pbuilderrc_rU7z --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cGr7VG6O/b1 --logfile b1/build.log stacks_2.68+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.cGr7VG6O/pbuilderrc_Ubcb --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cGr7VG6O/b2 --logfile b2/build.log stacks_2.68+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 6.1.0-25-armmp-lpae #1 SMP Debian 6.1.106-3 (2024-08-26) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21347/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -207,7 +239,7 @@ Get: 81 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2 [81.8 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.20-3 [620 kB] -Fetched 35.3 MB in 3s (13.5 MB/s) +Fetched 35.3 MB in 1s (23.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19491 files and directories currently installed.) @@ -554,7 +586,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/stacks-2.68+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 > ../stacks_2.68+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/stacks-2.68+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 > ../stacks_2.68+dfsg-1_source.changes dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.68+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -662,7 +698,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg' @@ -672,6 +708,7 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc In file included from /usr/include/c++/14/set:62, from src/constants.h:43, from src/ustacks.h:24, @@ -689,7 +726,9 @@ 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc In file included from /usr/include/c++/14/map:63, from src/constants.h:44: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', @@ -758,6 +797,7 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -806,6 +846,7 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/input.o src/input.cc /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, @@ -895,16 +936,12 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/input.o src/input.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/models.o src/models.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc src/MetaPopInfo.cc: In member function 'void MetaPopInfo::fill_pop_indexes(std::map >&) const': src/MetaPopInfo.cc:427:30: warning: narrowing conversion of 'i' from 'std::size_t' {aka 'unsigned int'} to 'int' [-Wnarrowing] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); @@ -924,7 +961,6 @@ /usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc @@ -936,6 +972,32 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc +In file included from /usr/include/c++/14/regex:52, + from src/sstacks.cc:25: +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': +/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/regex:55: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': +/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' changed in GCC 7.1 + 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 +In file included from /usr/include/c++/14/bits/stl_algo.h:61: +/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Distance = int; _Tp = pair<__cxx11::basic_string, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': +/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc +/usr/include/c++/14/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>&}; _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from src/constants.h:53, from src/MetaPopInfo.h:8, @@ -982,6 +1044,15 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4804:18, inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9: @@ -1002,45 +1073,11 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/regex:52, - from src/sstacks.cc:25: -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': -/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/regex:55: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': -/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' changed in GCC 7.1 - 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 -In file included from /usr/include/c++/14/bits/stl_algo.h:61: -/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Distance = int; _Tp = pair<__cxx11::basic_string, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]': -/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>&}; _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -1126,7 +1163,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/write.o src/write.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc @@ -1134,6 +1170,8 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/bootstrap.o src/bootstrap.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc src/export_formats.cc: In member function 'virtual int PhylipVarAllExport::post_processing()': src/export_formats.cc:2458:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] 2458 | sprintf(s, "%11lu", this->_seq_len); @@ -1180,10 +1218,15 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc +src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()': +src/Hwp.cc:383:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] + 383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long unsigned int std::size_t {aka unsigned int} + | %*u In file included from /usr/include/c++/14/map:62, from src/PopSum.h:27, from src/PopSum.cc:21: @@ -1207,90 +1250,7 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', - inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = HapStat]' at src/bootstrap.h:268:39, - inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: -/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2028 | return std::__upper_bound(__first, __last, __val, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 2029 | __gnu_cxx::__ops::__val_less_iter()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', - inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = SumStat]' at src/bootstrap.h:268:39, - inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: -/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2028 | return std::__upper_bound(__first, __last, __val, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 2029 | __gnu_cxx::__ops::__val_less_iter()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()': -src/Hwp.cc:383:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] - 383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long unsigned int std::size_t {aka unsigned int} - | %*u -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', - inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = PopPair]' at src/bootstrap.h:268:39, - inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: -/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2028 | return std::__upper_bound(__first, __last, __val, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 2029 | __gnu_cxx::__ops::__val_less_iter()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)' at src/PopSum.cc:2089:47: @@ -1409,27 +1369,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, - inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', - inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = LocStat]' at src/bootstrap.h:268:39, - inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: -/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2028 | return std::__upper_bound(__first, __last, __val, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 2029 | __gnu_cxx::__ops::__val_less_iter()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -1527,9 +1466,106 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', + inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = HapStat]' at src/bootstrap.h:268:39, + inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: +/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2028 | return std::__upper_bound(__first, __last, __val, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 2029 | __gnu_cxx::__ops::__val_less_iter()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', + inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = SumStat]' at src/bootstrap.h:268:39, + inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: +/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2028 | return std::__upper_bound(__first, __last, __val, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 2029 | __gnu_cxx::__ops::__val_less_iter()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', + inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = PopPair]' at src/bootstrap.h:268:39, + inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: +/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2028 | return std::__upper_bound(__first, __last, __val, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 2029 | __gnu_cxx::__ops::__val_less_iter()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, + inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', + inlined from 'double Bootstrap::pval(double, std::vector&) [with StatT = LocStat]' at src/bootstrap.h:268:39, + inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22: +/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2028 | return std::__upper_bound(__first, __last, __val, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 2029 | __gnu_cxx::__ops::__val_less_iter()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const': src/gstacks.cc:1369:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wformat=] 1369 | snprintf(c, id_len, "%luM", query.length()); @@ -1558,11 +1594,17 @@ rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp +ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp In file included from /usr/include/c++/14/algorithm:61, from src/constants.h:53, from src/gstacks.h:23, @@ -1571,8 +1613,6 @@ /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp In file included from /usr/include/c++/14/bits/stl_algobase.h:71, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3898, @@ -1600,8 +1640,6 @@ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 233 | __first + (__secondChild - 1))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -1629,8 +1667,6 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const::]' at /usr/include/c++/14/bits/stl_algo.h:4804:18, inlined from 'int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const' at src/gstacks.cc:1397:9: @@ -1798,16 +1834,16 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/gstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/tsv2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/libexec/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol @@ -1815,8 +1851,8 @@ dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-1_armhf.deb'. dpkg-deb: building package 'stacks' in '../stacks_2.68+dfsg-1_armhf.deb'. +dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../stacks_2.68+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../stacks_2.68+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1824,12 +1860,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1750/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1750/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/21347 and its subdirectories -I: Current time: Sat Sep 7 07:48:16 -12 2024 -I: pbuilder-time-stamp: 1725738496 +I: removing directory /srv/workspace/pbuilder/1750 and its subdirectories +I: Current time: Sun Sep 8 09:55:47 +14 2024 +I: pbuilder-time-stamp: 1725738947