Diff of the two buildlogs: -- --- b1/build.log 2024-12-08 12:30:00.399772643 +0000 +++ b2/build.log 2024-12-08 12:33:00.731597355 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 8 00:24:56 -12 2024 -I: pbuilder-time-stamp: 1733660696 +I: Current time: Mon Dec 9 02:30:40 +14 2024 +I: pbuilder-time-stamp: 1733661040 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17980/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22516/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 Dec 8 12:30 /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/22516/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22516/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='trixie' - 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=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='217aa34b0fbc40658507ea3b7c3896fe' - 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='17980' - PS1='# ' - PS2='> ' + INVOCATION_ID=456cceeec36b49be886b7d05625d994d + 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=22516 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.h3kG1BdV/pbuilderrc_dlv3 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h3kG1BdV/b1 --logfile b1/build.log rate4site_3.0.0-8.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.h3kG1BdV/pbuilderrc_nhyk --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h3kG1BdV/b2 --logfile b2/build.log rate4site_3.0.0-8.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 virt32c 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17980/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/22516/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] -Fetched 19.1 MB in 1s (24.5 MB/s) +Fetched 19.1 MB in 0s (40.4 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 ... 19685 files and directories currently installed.) @@ -269,7 +301,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes +I: user script /srv/workspace/pbuilder/22516/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/22516/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes dpkg-buildpackage: info: source package rate4site dpkg-buildpackage: info: source version 3.0.0-8 dpkg-buildpackage: info: source distribution unstable @@ -356,7 +392,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make all-recursive make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0' @@ -373,6 +409,7 @@ 507 | system(sysCall.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gainLossAlphabet.o gainLossAlphabet.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from someUtil.cpp:9: @@ -399,6 +436,7 @@ 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::vector > >' changed in GCC 7.1 +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1812 | __final_insertion_sort(_RandomAccessIterator __first, @@ -415,9 +453,9 @@ 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 -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o distribution.o distribution.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o readTree.o readTree.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o errorMsg.o errorMsg.cpp 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 'double computeFDRthreshold(Vdouble&, double, bool)' at someUtil.cpp:702:7: @@ -438,10 +476,10 @@ /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. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o readTree.o readTree.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o errorMsg.o errorMsg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nucleotide.o nucleotide.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o amino.o amino.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from someUtil.h:7, @@ -561,6 +599,7 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o doubleRep.o doubleRep.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void orderRankNoTies(const std::vector&, std::vector&)' at someUtil.cpp:858:20: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -579,6 +618,7 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'double computeMedian(const std::vector&)' at someUtil.cpp:90:6: @@ -605,10 +645,6 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o doubleRep.o doubleRep.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o uniDistribution.o uniDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o readDatMatrix.o readDatMatrix.cpp @@ -638,6 +674,8 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nucJC.o nucJC.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from readDatMatrix.h:6, @@ -646,22 +684,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)' at readDatMatrix.cpp:259:46: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:96:13: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from pijAccelerator.h:6, @@ -677,13 +699,20 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:52:52: + inlined from 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)' at readDatMatrix.cpp:259:46: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:53:13: + inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:96:13: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -710,13 +739,22 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:52:52: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:53:13: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::readCodonUsage(const std::string&, Vdouble&, const codon&)' at codon.cpp:460:19: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nucJC.o nucJC.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)' at codon.cpp:436:19: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -727,8 +765,6 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, @@ -739,6 +775,14 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)' at gtrModel.cpp:15:50: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from fromQtoPt.cpp:3: @@ -746,16 +790,22 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from distanceTable.cpp:3: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)' at gtrModel.cpp:15:50: + inlined from 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:256:17: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:256:17: + inlined from 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -779,22 +829,17 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o njConstrain.o njConstrain.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o numRec.o numRec.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from distanceTable.cpp:3: + from nj.h:8, + from nj.cpp:6: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o numRec.o numRec.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from numRec.cpp:6: @@ -802,14 +847,6 @@ /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, | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from nj.h:8, - from nj.cpp:6: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /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_less_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, @@ -823,12 +860,32 @@ 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 file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from uniformDistribution.h:22, + from uniformDistribution.cpp:3: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:33:15: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)' at nj.cpp:265:66: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp 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 'double performKSTest(const uniformDistribution&, Vdouble&)' at numRec.cpp:465:6: @@ -863,8 +920,6 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:167:14: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -885,50 +940,46 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from uniformDistribution.h:22, - from uniformDistribution.cpp:3: + from computePijComponent.cpp:4: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:33:15: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19: + inlined from 'void computePijHomSpec::resize(int)' at computePijComponent.h:19:48, + inlined from 'void computePijHomSpec::fillPij(double, const stochasticProcess&, int, bool)' at computePijComponent.cpp:14:11: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from computePijComponent.cpp:4: + from countTableComponent.h:6, + from countTableComponent.cpp:6: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computePijHomSpec::resize(int)' at computePijComponent.h:19:48, - inlined from 'void computePijHomSpec::fillPij(double, const stochasticProcess&, int, bool)' at computePijComponent.cpp:14:11: + inlined from 'void computePijHom::fillPij(const tree&, const stochasticProcess&, int, bool)' at computePijComponent.cpp:89:26: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computePijHomSpec::resize(int)' at computePijComponent.h:19:48, - inlined from 'void computePijHom::fillPij(const tree&, const stochasticProcess&, int, bool)' at computePijComponent.cpp:89:26: + inlined from 'void countTableComponentHom::countTableComponentAllocatePlace(int)' at countTableComponent.cpp:20:104: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from unObservableData.h:4, @@ -937,28 +988,13 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from countTableComponent.h:6, - from countTableComponent.cpp:6: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void countTableComponentHom::countTableComponentAllocatePlace(int)' at countTableComponent.cpp:20:104: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'unObservableData::unObservableData(const sequenceContainer&, const stochasticProcess*, gainLossAlphabet, int, int)' at unObservableData.cpp:12:31: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestAlpha.o bestAlpha.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, @@ -981,6 +1017,7 @@ /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++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp 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 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: @@ -1002,8 +1039,8 @@ /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. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputation.o likelihoodComputation.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from siteSpecificRate.h:6, @@ -1025,8 +1062,7 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from bestAlpha.h:6, - from bestAlpha.cpp:6: + from likelihoodComputation.cpp:3: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: @@ -1051,92 +1087,98 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:64:15: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:394:22: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:65:21: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:397:30: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from likelihoodComputation.cpp:3: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:394:22: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:402:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:397:30: + inlined from 'Vdouble likelihoodComputation::getLofPosPerCat(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:581:12: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:402:16: + inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:203:18: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:415:15: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:64:15: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:416:13: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:65:21: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:417:20: + inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)' at likelihoodComputation.cpp:181:18: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:418:20: + inlined from 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)' at likelihoodComputation.cpp:67:18: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getLofPosPerCat(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:581:12: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:415:15: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:203:18: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:416:13: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)' at likelihoodComputation.cpp:181:18: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:417:20: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)' at likelihoodComputation.cpp:67:18: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:418:20: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:129:29: + inlined from 'double likelihoodComputation::computeLikelihoodAndLikelihoodPerPosition(const sequenceContainer&, const tree&, const stochasticProcess&, Vdouble&)' at likelihoodComputation.cpp:559:17: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from bestAlpha.h:6, + from bestAlpha.cpp:6: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:150:16: + inlined from 'double likelihoodComputation::getPosteriorOfRatesAndLLPP(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:487:70: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::computeLikelihoodAndLikelihoodPerPosition(const sequenceContainer&, const tree&, const stochasticProcess&, Vdouble&)' at likelihoodComputation.cpp:559:17: + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1145,18 +1187,19 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getPosteriorOfRatesAndLLPP(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:487:70: + inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:129:29: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: + inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:150:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: + inlined from 'double likelihoodComputation::getPosteriorOfRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:453:70: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1180,17 +1223,19 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getPosteriorOfRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:453:70: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o hky.o hky.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, + from bblEM.h:5, + from bblEM.cpp:2: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o tamura92.o tamura92.cpp +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, from replacementModel.h:6, from hky.h:6, from hky.cpp:3: @@ -1204,7 +1249,7 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o tamura92.o tamura92.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1220,15 +1265,7 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from bblEM.h:5, - from bblEM.cpp:2: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, @@ -1237,6 +1274,7 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o talRandom.o talRandom.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bestGtrModelParams.h:6, @@ -1245,7 +1283,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bestHKYparam.h:6, @@ -1265,6 +1303,14 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from bestTamura92param.h:6, + from bestTamura92param.cpp:3: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestHKYparam.cpp:192:16: @@ -1276,31 +1322,46 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o talRandom.o talRandom.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:244:16: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeCounts.o computeCounts.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from bestTamura92param.h:6, - from bestTamura92param.cpp:3: + from computeSubstitutionCounts.h:4, + from computeSubstitutionCounts.cpp:1: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeCounts.o computeCounts.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:244:16: + inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: + inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:39:63: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from computeDownAlg.cpp:3: @@ -1310,20 +1371,18 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from computeSubstitutionCounts.h:4, - from computeSubstitutionCounts.cpp:1: + from computeUpAlg.cpp:3: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:39:63: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1349,36 +1408,13 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, - from computeUpAlg.cpp:3: + from computeUpAlgFactors.cpp:3: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, - inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, - inlined from 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:176:30: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: -/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1058 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, @@ -1387,31 +1423,21 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)' at computeUpAlg.cpp:33:19: + inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, + inlined from 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:176:30: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, - inlined from 'void suffStatGlobalGam::allocatePlace(int, int, int, int)' at suffStatComponent.h:193:54: + inlined from 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)' at computeUpAlg.cpp:33:19: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from computeUpAlgFactors.cpp:3: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)' at computeUpAlgFactors.cpp:128:16: @@ -1425,7 +1451,8 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:42:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1439,6 +1466,14 @@ 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, + inlined from 'void suffStatGlobalGam::allocatePlace(int, int, int, int)' at suffStatComponent.h:193:54: +/usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1058 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:84:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1450,8 +1485,10 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o matrixUtils.o matrixUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from matrixUtils.h:4, @@ -1466,6 +1503,15 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from simulateJumpsAbstract.h:4, + from simulateCodonsJumps.h:4, + from simulateCodonsJumps.cpp:1: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > add(const std::vector >&, const std::vector >&) [with _T = double]' at matrixUtils.h:107:19: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1476,15 +1522,6 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from simulateJumpsAbstract.h:4, - from simulateCodonsJumps.h:4, - from simulateCodonsJumps.cpp:1: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1501,17 +1538,6 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from computePosteriorExpectationOfSubstitutions.h:13, @@ -1520,29 +1546,43 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: + inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'virtual void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions.cpp:119:21: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp +In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, - inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:26:21: + inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'virtual void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions.cpp:119:21: + inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:26:21: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1555,10 +1595,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void simulateJumps::init()' at simulateJumps.cpp:21:27: @@ -1575,7 +1612,6 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from likelihoodComputationGL.h:4, @@ -1591,6 +1627,8 @@ 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likeDistPropEB.o likeDistPropEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bblEM.h:5, @@ -1599,7 +1637,9 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o likeDistPropEB.o likeDistPropEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o maseFormat.o maseFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from tree.cpp:2: @@ -1607,7 +1647,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, @@ -1623,24 +1663,20 @@ /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o maseFormat.o maseFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bblEMProportionalEB::allocatePlacePropEB()' at bblEMProportionalEB.cpp:106:31: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble bblEMProportionalEB::compute_bblEMPropEB(int, double, double, const double*)' at bblEMProportionalEB.cpp:41:17: /usr/include/c++/14/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1058 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp rm -f libphylo.a ar cru libphylo.a alphabet.o sequenceContainer.o sequence.o mulAlphabet.o someUtil.o logFile.o gainLossAlphabet.o pijAccelerator.o replacementModel.o distribution.o readTree.o errorMsg.o nucleotide.o amino.o geneticCodeHolder.o codon.o doubleRep.o evaluateCharacterFreq.o uniDistribution.o generalGammaDistribution.o readDatMatrix.o datMatrixHolder.o chebyshevAccelerator.o nucJC.o aaJC.o gtrModel.o fromQtoPt.o distanceTable.o nj.o njConstrain.o numRec.o uniformDistribution.o computePijComponent.o stochasticProcess.o suffStatComponent.o unObservableData.o likeDist.o countTableComponent.o fastStartTree.o likelihoodComputationFactors.o bestAlpha.o gammaDistribution.o siteSpecificRate.o likelihoodComputation.o recognizeFormat.o bblEM.o hky.o bestGtrModelParams.o tamura92.o bestHKYparam.o bestTamura92param.o talRandom.o computeSubstitutionCounts.o fromCountTableComponentToDistance.o computeCounts.o computeDownAlg.o computeUpAlg.o computeUpAlgFactors.o gammaUtilities.o seqContainerTreeMap.o treeUtil.o matrixUtils.o simulateCodonsJumps.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o multipleStochasticProcess.o simulateJumps.o simulateJumpsAbstract.o treeIt.o likelihoodComputationGL.o tree.o bblEMProportionalEB.o fromCountTableComponentToDistancePropEB.o likeDistPropEB.o bblLSProportionalEB.o phylipFormat.o maseFormat.o clustalFormat.o fastaFormat.o phylipSequentialFormat.o molphyFormat.o getRandomWeights.o nexusFormat.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1690,7 +1726,7 @@ make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' Making check in src/phylogeny make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' @@ -1706,7 +1742,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rate4site/ - make -j3 install DESTDIR=/build/reproducible-path/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0' Making install in src/phylogeny make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny' @@ -1768,12 +1804,14 @@ 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/22516/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22516/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/17980 and its subdirectories -I: Current time: Sun Dec 8 00:29:54 -12 2024 -I: pbuilder-time-stamp: 1733660994 +I: removing directory /srv/workspace/pbuilder/22516 and its subdirectories +I: Current time: Mon Dec 9 02:32:56 +14 2024 +I: pbuilder-time-stamp: 1733661176