Diff of the two buildlogs:
--
--- b1/build.log 2025-03-07 04:46:06.008235680 +0000
+++ b2/build.log 2025-03-07 05:36:01.657228094 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Thu Mar 6 16:37:12 -12 2025
-I: pbuilder-time-stamp: 1741322232
+I: Current time: Fri Mar 7 18:47:22 +14 2025
+I: pbuilder-time-stamp: 1741322842
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -29,52 +29,84 @@
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/26433/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/21718/tmp/hooks/D01_modify_environment starting
+debug: Running on cbxi4a.
+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 Mar 7 04:48 /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/21718/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/21718/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=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='e9063ffd76894823a7c2a9f215bf33d2'
- 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='26433'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=8e0a72793da94da2a1d087a3371b225f
+ 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=21718
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.EGMcf2TB/pbuilderrc_MszV --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.EGMcf2TB/b1 --logfile b1/build.log stacks_2.68+dfsg-2.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.EGMcf2TB/pbuilderrc_XKjq --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.EGMcf2TB/b2 --logfile b2/build.log stacks_2.68+dfsg-2.dsc'
+ SUDO_GID=113
+ SUDO_UID=107
+ 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 virt64b 6.1.0-31-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-23-armmp #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/26433/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/21718/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -220,7 +252,7 @@
Get: 96 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5+20250216-2 [82.8 kB]
Get: 97 http://deb.debian.org/debian unstable/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 98 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.21-1 [633 kB]
-Fetched 38.8 MB in 1s (60.9 MB/s)
+Fetched 38.8 MB in 3s (14.8 MB/s)
Preconfiguring packages ...
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 ... 19508 files and directories currently installed.)
@@ -627,7 +659,11 @@
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-2_source.changes
+I: user script /srv/workspace/pbuilder/21718/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/21718/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-2_source.changes
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.68+dfsg-2
dpkg-buildpackage: info: source distribution unstable
@@ -736,7 +772,7 @@
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'
@@ -746,6 +782,7 @@
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,
@@ -763,7 +800,9 @@
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<Aln*, std::vector<Aln> >' 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<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
@@ -808,6 +847,7 @@
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
+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::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
@@ -832,6 +872,7 @@
/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/input.o src/input.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<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
@@ -930,6 +971,8 @@
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __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/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
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = bool (*)(Aln, Aln)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from '_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0' at src/ustacks.cc:967:17:
@@ -969,16 +1012,10 @@
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' 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<int, std::pair<int, int> >&) 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}} );
@@ -998,7 +1035,6 @@
/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree<Nt2, std::pair<const Nt2, double>, std::_Select1st<std::pair<const Nt2, double> >, std::less<Nt2>, std::allocator<std::pair<const Nt2, double> > >::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
@@ -1010,6 +1046,32 @@
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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
+/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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_node_base*, std::_Rb_tree_node_base*> 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<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
+/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, 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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
+/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Distance = int; _Tp = pair<__cxx11::basic_string<char>, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
+/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignRes>&}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
+/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, 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,
@@ -1056,6 +1118,20 @@
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' 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<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const 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,
+ | ^~~~~~~~~~~~~~~~~~~~~~~~~
+/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<bool (*)(const AlignRes&, const 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
+/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const 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/file_io.o src/file_io.cc
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
@@ -1076,45 +1152,6 @@
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' 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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
-/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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_node_base*, std::_Rb_tree_node_base*> 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<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
-/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, 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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
-/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Distance = int; _Tp = pair<__cxx11::basic_string<char>, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
-/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignRes>&}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
-/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, 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<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const 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,
- | ^~~~~~~~~~~~~~~~~~~~~~~~~
-/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<bool (*)(const AlignRes&, const 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
-/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const 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_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
@@ -1200,7 +1237,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
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
@@ -1208,6 +1244,7 @@
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/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
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);
@@ -1216,6 +1253,7 @@
| | std::size_t {aka unsigned int}
| long unsigned int
| %11u
+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
In file included from /usr/include/c++/14/bits/stl_algo.h:61,
from /usr/include/c++/14/algorithm:61,
from src/constants.h:53,
@@ -1254,9 +1292,15 @@
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' 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:
@@ -1280,63 +1324,7 @@
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_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/Hwp.o src/Hwp.cc
-In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
- inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
- 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
- inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, std::vector<double> >' changed in GCC 7.1
-In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
- inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
- 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
- inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
- inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
- 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2089:47:
@@ -1455,48 +1443,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
-In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
- inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
- 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
- inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
- inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
- 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
- inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' changed in GCC 7.1
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
@@ -1505,6 +1451,7 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | 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/tsv2bam.o src/tsv2bam.cc
/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[](key_type&&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
@@ -1522,13 +1469,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
-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 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<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]',
inlined from 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)' at src/PopSum.cc:937:39:
/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' changed in GCC 7.1
@@ -1601,8 +1541,6 @@
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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<char>::size_type' {aka 'unsigned int'} [-Wformat=]
@@ -1620,6 +1558,104 @@
| long unsigned int std::size_t {aka unsigned int}
| %u
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/debruijn.o src/debruijn.cc
+In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
+ inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
+ 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
+ inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, std::vector<double> >' changed in GCC 7.1
+In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
+ inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
+ 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
+ inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
+ inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
+ 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
+ inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
+ 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
+ inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' 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<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
+ inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
+ 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<double*, std::vector<double> >' 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<double*, std::vector<double> >' 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<double*, vector<double> >; _Tp = double]',
+ inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [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<double*, std::vector<double> >' changed in GCC 7.1
+ 2028 | return std::__upper_bound(__first, __last, __val,
+ | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
+ 2029 | __gnu_cxx::__ops::__val_less_iter());
+ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/SuffixTree.o src/SuffixTree.cc
rm -f libcore.a
ar cr libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o
@@ -1634,6 +1670,12 @@
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,
@@ -1642,7 +1684,6 @@
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' 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
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:3906,
@@ -1670,7 +1711,6 @@
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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 process_shortreads src/process_shortreads.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<STAln*, vector<STAln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
@@ -1698,10 +1738,6 @@
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' 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 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 function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, vector<STAln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<STAln*, vector<STAln> >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)>]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const' at src/gstacks.cc:1397:9:
@@ -1870,17 +1906,17 @@
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/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/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/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/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
-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/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/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_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/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/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/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/clone_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/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/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/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/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined
@@ -1896,12 +1932,14 @@
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/21718/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/21718/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/26433 and its subdirectories
-I: Current time: Thu Mar 6 16:46:00 -12 2025
-I: pbuilder-time-stamp: 1741322760
+I: removing directory /srv/workspace/pbuilder/21718 and its subdirectories
+I: Current time: Fri Mar 7 19:35:56 +14 2025
+I: pbuilder-time-stamp: 1741325756