Diff of the two buildlogs: -- --- b1/build.log 2024-05-12 03:33:04.632534337 +0000 +++ b2/build.log 2024-05-12 03:39:13.292842863 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 11 15:29:46 -12 2024 -I: pbuilder-time-stamp: 1715484586 +I: Current time: Sun May 12 17:33:28 +14 2024 +I: pbuilder-time-stamp: 1715484808 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/27733/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22695/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 12 03:33 /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/22695/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22695/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(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='1d3ada79ff0243f3be3600d013019ad3' - 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='27733' - PS1='# ' - PS2='> ' + INVOCATION_ID=10873e922a404f93b9fd9980056ffe85 + 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=22695 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.0xrXu1if/pbuilderrc_lWvI --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.0xrXu1if/b1 --logfile b1/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+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.0xrXu1if/pbuilderrc_meES --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.0xrXu1if/b2 --logfile b2/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-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32z 6.1.0-21-armmp-lpae #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 10 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27733/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 10 18:08 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/22695/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -139,7 +171,7 @@ Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] -Fetched 18.4 MB in 0s (62.6 MB/s) +Fetched 18.4 MB in 0s (44.2 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 ... 19446 files and directories currently installed.) @@ -274,7 +306,11 @@ 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/22695/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/22695/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 @@ -361,7 +397,7 @@ 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' @@ -372,11 +408,11 @@ 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 sequence.o sequence.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 mulAlphabet.o mulAlphabet.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 someUtil.o someUtil.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 logFile.o logFile.cpp someUtil.cpp: In function 'void createDir(const std::string&, const std::string&)': someUtil.cpp:507:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 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 logFile.o logFile.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 gainLossAlphabet.o gainLossAlphabet.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, @@ -447,6 +483,7 @@ 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 In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from someUtil.h:7, @@ -455,6 +492,7 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 codon.o codon.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = vecElem; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -610,8 +648,6 @@ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | 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 @@ -643,6 +679,8 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/13/vector:72, from definitions.h:18, from readDatMatrix.h:6, @@ -651,24 +689,19 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from definitions.h:18, - from pijAccelerator.h:6, - from chebyshevAccelerator.h:6, - from chebyshevAccelerator.cpp:3: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void chebyshevAccelerator::chebft(Vdouble&, int, int, int)' at chebyshevAccelerator.cpp:94:10: + inlined from 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)' at readDatMatrix.cpp:259:46: /usr/include/c++/13/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++/13/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: + inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:52:52: +/usr/include/c++/13/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++/13/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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -680,61 +713,65 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from definitions.h:18, + from pijAccelerator.h:6, + from chebyshevAccelerator.h:6, + from chebyshevAccelerator.cpp:3: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | 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 gtrModel.o gtrModel.cpp In file included from /usr/include/c++/13/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++/13/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++/13/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: -/usr/include/c++/13/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 chebyshevAccelerator::chebft(Vdouble&, int, int, int)' at chebyshevAccelerator.cpp:94:10: /usr/include/c++/13/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 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:49:33: + inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: /usr/include/c++/13/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 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:50:43: + inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:96:13: /usr/include/c++/13/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 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:51:47: + inlined from 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:49:33: /usr/include/c++/13/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: + inlined from 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:50:43: /usr/include/c++/13/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: + inlined from 'chebyshevAccelerator::chebyshevAccelerator(replacementModel*, int, int, int, double, double)' at chebyshevAccelerator.cpp:51:47: /usr/include/c++/13/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 fromQtoPt.o fromQtoPt.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++/13/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 double codonUtility::calcCodonAdaptationIndex(const sequenceContainer&, const Vdouble&, Vdouble&)' at codon.cpp:517:17: /usr/include/c++/13/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 +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++/13/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -744,6 +781,20 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/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++/13/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++/13/vector:72, + from definitions.h:18, + from distanceTable.cpp:3: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from fromQtoPt.cpp:3: @@ -753,7 +804,7 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: /usr/include/c++/13/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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -763,6 +814,7 @@ /usr/include/c++/13/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 njConstrain.o njConstrain.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void q2pt::fillFromRateMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:27:50: /usr/include/c++/13/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -783,23 +835,8 @@ /usr/include/c++/13/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 -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 -In file included from /usr/include/c++/13/vector:72, - from definitions.h:18, - from distanceTable.cpp:3: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/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++/13/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++/13/vector:72, from definitions.h:18, from nj.h:8, @@ -828,7 +865,26 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: 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 uniformDistribution.o uniformDistribution.cpp +In file included from /usr/include/c++/13/vector:72, + from definitions.h:18, + from uniformDistribution.h:22, + from uniformDistribution.cpp:3: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/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++/13/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++/13/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 file included from /usr/include/c++/13/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: @@ -863,33 +919,14 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from definitions.h:18, - from uniformDistribution.h:22, - from uniformDistribution.cpp:3: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/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++/13/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++/13/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++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeEigenSystem(VVdouble&, VVdouble&, Vdouble&)' at numRec.cpp:443:20: /usr/include/c++/13/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 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 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++/13/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -910,7 +947,6 @@ /usr/include/c++/13/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 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++/13/vector:72, @@ -920,6 +956,7 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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++/13/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, @@ -927,21 +964,6 @@ /usr/include/c++/13/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 computePijHomSpec::resize(int)' at computePijComponent.h:19:48, - inlined from 'void computePijHom::fillPij(const tree&, const stochasticProcess&, int, bool)' at computePijComponent.cpp:89:26: -/usr/include/c++/13/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 -In file included from /usr/include/c++/13/vector:72, - from definitions.h:18, - from unObservableData.h:4, - from unObservableData.cpp:1: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from countTableComponent.h:6, @@ -950,22 +972,28 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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++/13/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++/13/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++/13/vector:66: +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 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: + 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: /usr/include/c++/13/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++/13/vector:72, + from definitions.h:18, + from unObservableData.h:4, + from unObservableData.cpp:1: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | 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 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++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from fastStartTree.cpp:15: @@ -986,6 +1014,14 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | 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 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++/13/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++/13/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 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++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: @@ -1009,6 +1045,7 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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++/13/vector:72, from definitions.h:18, from bestAlpha.h:6, @@ -1017,123 +1054,143 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 bblEM.o bblEM.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, - from siteSpecificRate.h:6, - from siteSpecificRate.cpp:3: + from likelihoodComputation.cpp:3: /usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:20:15: -/usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:21:21: + 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++/13/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:64:15: + 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++/13/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:402:16: /usr/include/c++/13/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++/13/vector:72, from definitions.h:18, - from likelihoodComputation.cpp:3: + from siteSpecificRate.h:6, + from siteSpecificRate.cpp:3: /usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: 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 sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:20:15: /usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:21:21: /usr/include/c++/13/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 '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++/13/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 '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++/13/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++/13/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 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)' at likelihoodComputation.cpp:67:18: /usr/include/c++/13/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:397:30: + inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)' at likelihoodComputation.cpp:181:18: /usr/include/c++/13/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++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:151:15: + inlined from 'Vdouble likelihoodComputation::getLofPosPerCat(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:581:12: /usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:152:13: + 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++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:153:20: + 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++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:154:20: + 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++/13/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++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:151:15: /usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:152:13: /usr/include/c++/13/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 sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:153:20: /usr/include/c++/13/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_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)' at siteSpecificRate.cpp:323:33: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:154:20: /usr/include/c++/13/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: +/usr/include/c++/13/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); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 450 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:380:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:530:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)' at likelihoodComputation.cpp:350:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/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: @@ -1146,73 +1203,61 @@ 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 'void computeEB_EXP_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)' at siteSpecificRate.cpp:323:33: /usr/include/c++/13/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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 450 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:380:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __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_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:291:15: + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: /usr/include/c++/13/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_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:292:13: + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: /usr/include/c++/13/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_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:293:20: + inlined from 'double likelihoodComputation::getPosteriorOfRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:453:70: /usr/include/c++/13/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_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:294:20: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:291:15: /usr/include/c++/13/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>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:530:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)' at likelihoodComputation.cpp:350:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __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 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:292:13: /usr/include/c++/13/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 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:293:20: /usr/include/c++/13/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: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:294:20: /usr/include/c++/13/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 +In file included from /usr/include/c++/13/vector:72, + from definitions.h:18, + from bblEM.h:5, + from bblEM.cpp:2: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ 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: /usr/include/c++/13/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 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 +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++/13/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1228,7 +1273,7 @@ /usr/include/c++/13/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++/13/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1238,29 +1283,13 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from definitions.h:18, - from bblEM.h:5, - from bblEM.cpp:2: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'tamura92::tamura92(double, double)' at tamura92.cpp:12:14: /usr/include/c++/13/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++/13/vector:72, - from definitions.h:18, - from bestGtrModelParams.h:6, - from bestGtrModelParams.cpp:3: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | 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++/13/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, @@ -1271,13 +1300,30 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, + from bestGtrModelParams.h:6, + from bestGtrModelParams.cpp:3: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | 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 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++/13/vector:72, + from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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++/13/vector:72, + from definitions.h:18, + from bestTamura92param.h:6, + from bestTamura92param.cpp:3: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:218:16: @@ -1300,18 +1346,6 @@ /usr/include/c++/13/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++/13/vector:72, - from definitions.h:18, - from bestTamura92param.h:6, - from bestTamura92param.cpp:3: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | 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 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 -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 In file included from /usr/include/c++/13/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: @@ -1323,6 +1357,8 @@ /usr/include/c++/13/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 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++/13/vector:72, @@ -1333,6 +1369,17 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/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: +/usr/include/c++/13/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: +/usr/include/c++/13/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++/13/vector:72, from definitions.h:18, from computeDownAlg.cpp:3: @@ -1342,23 +1389,25 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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 suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'void computeDownAlg::fillComputeDownSpecificRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&, double)' at computeDownAlg.cpp:120:19: /usr/include/c++/13/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::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: /usr/include/c++/13/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++/13/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 'void computeDownAlg::fillComputeDownSpecificRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&, double)' at computeDownAlg.cpp:120:19: + inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:14:19: /usr/include/c++/13/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++/13/vector:72, from definitions.h:18, from computeUpAlg.cpp:3: @@ -1367,29 +1416,19 @@ 529 | 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 computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: -/usr/include/c++/13/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 computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:14:19: + inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:63:19: /usr/include/c++/13/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 computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:63:19: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: /usr/include/c++/13/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++/13/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 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)' at computeUpAlg.cpp:110:19: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: /usr/include/c++/13/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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1401,34 +1440,22 @@ /usr/include/c++/13/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++/13/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++/13/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++/13/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 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)' at computeUpAlg.cpp:33:19: + inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)' at computeUpAlg.cpp:110:19: /usr/include/c++/13/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 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++/13/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 -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++/13/vector:72, from definitions.h:18, from computeUpAlgFactors.cpp:3: @@ -1436,6 +1463,7 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 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 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', @@ -1474,8 +1502,26 @@ /usr/include/c++/13/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: +/usr/include/c++/13/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 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++/13/vector:72, + from definitions.h:18, + from simulateJumpsAbstract.h:4, + from simulateCodonsJumps.h:4, + from simulateCodonsJumps.cpp:1: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from matrixUtils.h:4, @@ -1484,6 +1530,10 @@ /usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 450 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 450 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDoubleVecFromFile(Vdouble&, std::string)' at matrixUtils.cpp:198:17: @@ -1514,19 +1564,6 @@ /usr/include/c++/13/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++/13/vector:72, - from definitions.h:18, - from simulateJumpsAbstract.h:4, - from simulateCodonsJumps.h:4, - from simulateCodonsJumps.cpp:1: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 450 | 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++/13/bits/stl_vector.h:1058:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1542,11 +1579,6 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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++/13/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++/13/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 simulateCodonsJumps::init()' at simulateCodonsJumps.cpp:20:27: @@ -1563,17 +1595,11 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __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++/13/vector:72, - from definitions.h:18, - from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | 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++/13/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++/13/vector:72, from definitions.h:18, from computePosteriorExpectationOfSubstitutions.h:13, @@ -1582,25 +1608,33 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 In file included from /usr/include/c++/13/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++/13/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++/13/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++/13/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 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 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 'virtual void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions.cpp:119:21: /usr/include/c++/13/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 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++/13/vector:72, + from definitions.h:18, + from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | 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++/13/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1610,16 +1644,28 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/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++/13/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++/13/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 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 bblEMProportionalEB.o bblEMProportionalEB.cpp +In file included from /usr/include/c++/13/vector:72, + from definitions.h:18, + from likelihoodComputationGL.h:4, + from likelihoodComputationGL.cpp:1: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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: @@ -1636,16 +1682,6 @@ /usr/include/c++/13/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 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++/13/vector:72, - from definitions.h:18, - from likelihoodComputationGL.h:4, - from likelihoodComputationGL.cpp:1: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:450:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 450 | vector<_Tp, _Alloc>:: @@ -1662,6 +1698,9 @@ 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 +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 In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bblEM.h:5, @@ -1670,8 +1709,8 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 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 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++/13/vector:72, from definitions.h:18, from tree.cpp:2: @@ -1679,6 +1718,7 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | 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 fastaFormat.o fastaFormat.cpp In file included from /usr/include/c++/13/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, @@ -1688,30 +1728,26 @@ /usr/include/c++/13/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 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void tree::getTreeDistanceTableAndNames(VVdouble&, std::vector >&) const' at tree.cpp:453:21: /usr/include/c++/13/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 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++/13/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++/13/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') @@ -1733,12 +1769,6 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void rate4site::normalizeRates()' at rate4site.cpp:730:25: -/usr/include/c++/13/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++/13/vector:72, from ../../src/phylogeny/definitions.h:18, from rate4site.h:20, @@ -1753,15 +1783,21 @@ /usr/include/c++/13/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++ -I../../src/phylogeny/ -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 -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void rate4site::normalizeRates()' at rate4site.cpp:730:25: +/usr/include/c++/13/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++ -I../../src/phylogeny/ -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 -Wl,-z,relro -Wl,-z,now -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a +g++ -I../../src/phylogeny/ -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 -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0' make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0' 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' @@ -1777,7 +1813,7 @@ 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' @@ -1820,14 +1856,14 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/rate4site/usr/bin/rate4site_doublerep contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/rate4site/usr/bin/rate4site contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/rate4site/usr/bin/rate4site_doublerep contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_armhf.deb'. dpkg-deb: building package 'rate4site' in '../rate4site_3.0.0-8_armhf.deb'. +dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../rate4site_3.0.0-8_armhf.buildinfo dpkg-genchanges --build=binary -O../rate4site_3.0.0-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1835,12 +1871,14 @@ 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/22695/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22695/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/27733 and its subdirectories -I: Current time: Sat May 11 15:33:00 -12 2024 -I: pbuilder-time-stamp: 1715484780 +I: removing directory /srv/workspace/pbuilder/22695 and its subdirectories +I: Current time: Sun May 12 17:39:08 +14 2024 +I: pbuilder-time-stamp: 1715485148