Diff of the two buildlogs: -- --- b1/build.log 2025-01-12 05:54:02.693014820 +0000 +++ b2/build.log 2025-01-12 06:28:17.862829484 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 11 17:37:00 -12 2025 -I: pbuilder-time-stamp: 1736660220 +I: Current time: Sun Jan 12 19:54:44 +14 2025 +I: pbuilder-time-stamp: 1736661284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/32626/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4131/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 Jan 12 05:55 /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/4131/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4131/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='8e01230d5da1407fbf1c4d11168e56b8' - 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='32626' - PS1='# ' - PS2='> ' + INVOCATION_ID=4459611a24634135bfd60f9423ed7514 + 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=4131 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.HHFUF2XE/pbuilderrc_c87e --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.HHFUF2XE/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/pbuilderrc_3rzU --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.HHFUF2XE/b2 --logfile b2/build.log garli_2.1-9.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 virt64c 6.1.0-29-arm64 #1 SMP Debian 6.1.123-1 (2025-01-02) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-29-armmp-lpae #1 SMP Debian 6.1.123-1 (2025-01-02) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/32626/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/4131/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -163,7 +195,7 @@ Get: 50 http://deb.debian.org/debian trixie/main armhf libncl-dev armhf 2.1.21+git20210811.b1213a7-6 [537 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf mpi-default-dev armhf 1.18 [3372 B] Get: 52 http://deb.debian.org/debian trixie/main armhf ncl-tools armhf 2.1.21+git20210811.b1213a7-6 [130 kB] -Fetched 36.0 MB in 1s (28.4 MB/s) +Fetched 36.0 MB in 2s (21.8 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19567 files and directories currently installed.) @@ -393,7 +425,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/garli-2.1/ && 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 > ../garli_2.1-9_source.changes +I: user script /srv/workspace/pbuilder/4131/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4131/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/garli-2.1/ && 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 > ../garli_2.1-9_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable @@ -495,8 +531,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -565,7 +601,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -574,6 +610,29 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -618,6 +677,23 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -674,31 +750,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i >; _ForwardIterator = ProcessedNxsToken*]': @@ -1205,29 +1264,7 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -1271,7 +1308,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -1279,41 +1315,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1368,6 +1369,42 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1424,6 +1461,30 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: @@ -1469,13 +1530,7 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1487,12 +1542,16 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from population.cpp:25: + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1520,32 +1579,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1602,62 +1636,7 @@ tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from mpitrick.cpp:27: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from mpitrick.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_function.h:1435: -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1766,6 +1746,62 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from mpitrick.cpp:27: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from mpitrick.cpp:21: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -1961,6 +2020,22 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2013,11 +2088,36 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i >; _ForwardIterator = ProcessedNxsToken*]': @@ -2532,14 +2575,6 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -2644,6 +2679,8 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -2679,6 +2716,30 @@ model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2735,29 +2796,6 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: @@ -2815,24 +2853,8 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 536870911] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2852,11 +2874,23 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 536870911] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.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 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2913,28 +2947,7 @@ tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from treenode.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -3021,6 +3034,29 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from treenode.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests @@ -3037,7 +3073,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -5557,7 +5593,7 @@ pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 6 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5707,7 +5743,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6004,7 +6040,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 0 minutes and 48 seconds +Time used = 0 hours, 1 minutes and 34 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6156,7 +6192,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 35 seconds +Time used = 0 hours, 1 minutes and 15 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6360,7 +6396,7 @@ pass 75: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2333 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6730,7 +6766,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6885,7 +6921,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7052,7 +7088,7 @@ pass 15: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 11 seconds +Time used = 0 hours, 0 minutes and 26 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7306,7 +7342,7 @@ pass 34: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 13 seconds +Time used = 0 hours, 0 minutes and 17 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7731,7 +7767,7 @@ pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8786,7 +8822,7 @@ pass 13: -493.6676 (branch= 0.0000) Looking for minimum length branches... Final score = -493.6676 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9276,7 +9312,7 @@ pass 494: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 17 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9540,7 +9576,7 @@ pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 -Time used = 0 hours, 0 minutes and 13 seconds +Time used = 0 hours, 0 minutes and 19 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9832,7 +9868,7 @@ pass 488: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 18 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10123,7 +10159,7 @@ pass 489: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3586 -Time used = 0 hours, 0 minutes and 11 seconds +Time used = 0 hours, 0 minutes and 21 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -12827,9 +12863,6 @@ lnL after optimization: -93.4068 gen current_lnL precision last_tree_imp 0 -93.4068 0.500 0 -100 -93.0240 0.500 0 -200 -91.3705 0.500 199 -300 -90.7565 0.500 215 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12926,9 +12959,12 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 370, seed 1797603490, best lnL -90.631 +Bootstrap rep 1 (of 1) generation 87, seed 1360521649, best lnL -93.081 gen current_lnL precision last_tree_imp -370 -90.6312 0.500 215 +87 -93.0811 0.500 0 +100 -93.0240 0.500 0 +200 -91.3705 0.500 199 +300 -90.7565 0.500 215 400 -90.4959 0.500 215 500 -90.3850 0.500 215 600 -90.2906 0.500 215 @@ -13105,8 +13141,6 @@ lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 -100 -112.9555 0.500 84 -200 -112.4964 0.500 84 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13193,9 +13227,11 @@ STARTING RUN Restarting from checkpoint... - generation 246, seed 1608648735, best lnL -112.441 + generation 52, seed 756044145, best lnL -113.189 gen current_lnL precision last_tree_imp -246 -112.4415 0.500 84 +52 -113.1891 0.500 49 +100 -112.9555 0.500 84 +200 -112.4964 0.500 84 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 @@ -13373,13 +13409,6 @@ 100 -113.6842 0.500 91 200 -112.5462 0.500 160 300 -112.1250 0.500 160 -400 -111.8851 0.500 160 -500 -111.7755 0.500 160 -600 -111.6975 0.500 563 -700 -111.6876 0.500 563 -800 -111.6844 0.500 563 -900 -111.6835 0.500 563 -1000 -111.6829 0.500 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13465,11 +13494,19 @@ STARTING RUN Restarting from checkpoint... - generation 1091, seed 462149512, best lnL -111.683 + generation 399, seed 1284859412, best lnL -111.885 gen current_lnL precision last_tree_imp -1091 -111.6827 0.500 563 +399 -111.8851 0.500 160 +400 -111.8851 0.500 160 +500 -111.7755 0.500 160 +600 -111.6975 0.500 563 +700 -111.6876 0.500 563 +800 -111.6844 0.500 563 +900 -111.6835 0.500 563 +1000 -111.6829 0.500 563 +NOTE: ****Specified generation limit (1000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -13486,23 +13523,30 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6827 +Replicate 1 : -111.6829 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.619 +rep 1: 2.616 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf @@ -13625,7 +13669,6 @@ lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 -10 -207.1401 0.500 10 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13712,9 +13755,10 @@ STARTING RUN Restarting from checkpoint... - generation 13, seed 1603481258, best lnL -206.464 + generation 1, seed 1398556760, best lnL -208.980 gen current_lnL precision last_tree_imp -13 -206.4639 0.500 13 +1 -208.9797 0.500 0 +10 -207.1401 0.500 10 20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 @@ -13908,7 +13952,6 @@ lnL after optimization: -195.4001 gen current_lnL precision last_tree_imp 0 -195.4001 0.500 0 -10 -195.3555 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13996,9 +14039,10 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 12, seed 1380786643, best lnL -195.348 +Bootstrap rep 1 (of 1) generation 1, seed 1398556760, best lnL -195.400 gen current_lnL precision last_tree_imp -12 -195.3480 0.500 0 +1 -195.4001 0.500 0 +10 -195.3555 0.500 0 20 -195.3342 0.500 0 30 -195.2777 0.500 0 40 -195.2556 0.500 0 @@ -14213,13 +14257,6 @@ Optimizing parameters... improved 0.940 lnL Optimizing branchlengths... improved 0.000 lnL 600 -3354.6612 0.255 0 -700 -3354.3974 0.255 0 -800 -3354.0880 0.255 0 -900 -3353.8938 0.255 0 -1000 -3353.6942 0.255 0 -Optimization precision reduced - Optimizing parameters... improved 0.833 lnL - Optimizing branchlengths... improved 0.085 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14323,75 +14360,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1050, seed 1689402887, best lnL -3352.754 +Search rep 1 (of 2) generation 620, seed 1405986049, best lnL -3354.517 gen current_lnL precision last_tree_imp -1050 -3352.7536 0.010 0 -1100 -3352.7168 0.010 0 -1200 -3352.6373 0.010 0 -1300 -3352.5144 0.010 0 -1400 -3352.4046 0.010 0 -1500 -3352.3996 0.010 0 -1600 -3352.2933 0.010 0 -1700 -3352.2857 0.010 0 -1800 -3352.2040 0.010 0 +620 -3354.5168 0.255 0 +700 -3354.3974 0.255 0 +800 -3354.0880 0.255 0 +900 -3353.8938 0.255 0 +1000 -3353.6942 0.255 0 +Optimization precision reduced + Optimizing parameters... improved 0.833 lnL + Optimizing branchlengths... improved 0.085 lnL NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3352.0486 +Current score = -3352.7586 Performing final optimizations... -pass 1 : -3351.7984 (branch= 0.0075 alpha= 0.0156 pinv= 0.0206 eq freqs= 0.0127 rel rates= 0.1846 subset rates= 0.0092) -pass 2 : -3351.5648 (branch= 0.0159 alpha= 0.0110 pinv= 0.0186 eq freqs= 0.0066 rel rates= 0.1798 subset rates= 0.0016) -pass 3 : -3351.3672 (branch= 0.0083 alpha= 0.0170 pinv= 0.0161 eq freqs= 0.0088 rel rates= 0.1463 subset rates= 0.0011) -pass 4 : -3351.2022 (branch= 0.0091 alpha= 0.0137 pinv= 0.0152 eq freqs= 0.0013 rel rates= 0.1237 subset rates= 0.0021) -pass 5 : -3351.0655 (branch= 0.0092 alpha= 0.0130 pinv= 0.0143 eq freqs= 0.0004 rel rates= 0.0977 subset rates= 0.0021) -pass 6 : -3350.9493 (branch= 0.0060 alpha= 0.0117 pinv= 0.0135 eq freqs= 0.0005 rel rates= 0.0829 subset rates= 0.0017) -pass 7 : -3350.8512 (branch= 0.0036 alpha= 0.0109 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0696 subset rates= 0.0013) -pass 8 : -3350.7661 (branch= 0.0027 alpha= 0.0103 pinv= 0.0114 eq freqs= 0.0001 rel rates= 0.0596 subset rates= 0.0010) -pass 9 : -3350.6938 (branch= 0.0019 alpha= 0.0097 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0501 subset rates= 0.0000) -pass 10: -3350.6289 (branch= 0.0005 alpha= 0.0093 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0438 subset rates= 0.0011) -pass 11: -3350.5747 (branch= 0.0009 alpha= 0.0088 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0358 subset rates= 0.0000) -pass 12: -3350.5289 (branch= 0.0002 alpha= 0.0081 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0297 subset rates= 0.0000) -pass 13: -3350.4890 (branch= 0.0001 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0252 subset rates= 0.0000) -pass 14: -3350.4544 (branch= 0.0000 alpha= 0.0069 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0214 subset rates= 0.0000) -pass 15: -3350.4246 (branch= 0.0000 alpha= 0.0062 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0180 subset rates= 0.0000) -pass 16: -3350.3987 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0000) -pass 17: -3350.3763 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0130 subset rates= 0.0000) -pass 18: -3350.3570 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0110 subset rates= 0.0000) -pass 19: -3350.3403 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0094 subset rates= 0.0000) -pass 20: -3350.3258 (branch= 0.0000 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0080 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2547 (branch= 0.0000 alpha= 0.0172 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0382 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2384 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0089 subset rates= 0.0000) +pass 1 : -3352.3646 (branch= 0.0088 alpha= 0.0079 pinv= 0.0182 eq freqs= 0.0092 rel rates= 0.3425 subset rates= 0.0075) +pass 2 : -3352.0069 (branch= 0.0517 alpha= 0.0101 pinv= 0.0174 eq freqs= 0.0058 rel rates= 0.2560 subset rates= 0.0167) +pass 3 : -3351.7323 (branch= 0.0317 alpha= 0.0110 pinv= 0.0171 eq freqs= 0.0015 rel rates= 0.2045 subset rates= 0.0088) +pass 4 : -3351.4976 (branch= 0.0208 alpha= 0.0119 pinv= 0.0162 eq freqs= 0.0033 rel rates= 0.1762 subset rates= 0.0064) +pass 5 : -3351.3055 (branch= 0.0144 alpha= 0.0113 pinv= 0.0152 eq freqs= 0.0007 rel rates= 0.1455 subset rates= 0.0049) +pass 6 : -3351.1478 (branch= 0.0094 alpha= 0.0112 pinv= 0.0143 eq freqs= 0.0003 rel rates= 0.1189 subset rates= 0.0036) +pass 7 : -3351.0117 (branch= 0.0056 alpha= 0.0106 pinv= 0.0132 eq freqs= 0.0006 rel rates= 0.1036 subset rates= 0.0026) +pass 8 : -3350.8959 (branch= 0.0051 alpha= 0.0104 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.0863 subset rates= 0.0015) +pass 9 : -3350.8010 (branch= 0.0028 alpha= 0.0102 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0705 subset rates= 0.0000) +pass 10: -3350.7161 (branch= 0.0006 alpha= 0.0100 pinv= 0.0108 eq freqs= 0.0002 rel rates= 0.0615 subset rates= 0.0018) +pass 11: -3350.6474 (branch= 0.0018 alpha= 0.0094 pinv= 0.0098 eq freqs= 0.0003 rel rates= 0.0473 subset rates= 0.0000) +pass 12: -3350.5897 (branch= 0.0004 alpha= 0.0083 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0406 subset rates= 0.0000) +pass 13: -3350.5388 (branch= 0.0001 alpha= 0.0080 pinv= 0.0075 eq freqs= 0.0001 rel rates= 0.0342 subset rates= 0.0010) +pass 14: -3350.4975 (branch= 0.0006 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0266 subset rates= 0.0000) +pass 15: -3350.4619 (branch= 0.0001 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0231 subset rates= 0.0000) +pass 16: -3350.4309 (branch= 0.0000 alpha= 0.0059 pinv= 0.0054 eq freqs= 0.0001 rel rates= 0.0196 subset rates= 0.0000) +pass 17: -3350.4039 (branch= 0.0000 alpha= 0.0053 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0168 subset rates= 0.0000) +pass 18: -3350.3806 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0142 subset rates= 0.0000) +pass 19: -3350.3605 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0121 subset rates= 0.0000) +pass 20: -3350.3431 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0103 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2583 (branch= 0.0000 alpha= 0.0190 pinv= 0.0173 eq freqs= 0.0001 rel rates= 0.0484 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2389 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0112 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2348 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) +pass 50: -3350.2345 (branch= 0.0000 alpha= 0.0008 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2340 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) +pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 71: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 74: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2338 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3350.2333 +Time used so far = 0 hours, 0 minutes and 17 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.112, AG = 10.402, AT = 2.687, CG = 0.001, CT = 21.855, GT = 1.000 + AC = 3.111, AG = 10.402, AT = 2.687, CG = 0.001, CT = 21.881, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5793 + 0.5785 with an invariant (invariable) site category, proportion estimated - 0.3662 + 0.3660 Substitution rate categories under this model: rate proportion - 0.0000 0.3662 - 0.0489 0.1585 - 0.3006 0.1585 - 0.8704 0.1585 - 2.7801 0.1585 + 0.0000 0.3660 + 0.0487 0.1585 + 0.3001 0.1585 + 0.8699 0.1585 + 2.7813 0.1585 Model 2 Number of states = 2 (binary data) @@ -14416,20 +14452,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2338 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2333 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.112 10.4 2.687 0.001 21.85 1 0.333 0.222 0.157 0.288 0.579 0.366 +rep 1: 3.111 10.4 2.687 0.001 21.88 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.787 1.820 0.180 +rep 1: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14576,7 +14612,6 @@ gen current_lnL precision last_tree_imp 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 -200 -3324.7543 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14677,70 +14712,68 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 259, seed 526245243, best lnL -3324.603 +Search rep 1 (of 2) generation 116, seed 484836576, best lnL -3324.921 gen current_lnL precision last_tree_imp -259 -3324.6034 0.500 1 -300 -3324.3007 0.500 1 -400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 +116 -3324.9211 0.500 1 +200 -3324.7543 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3323.3791 +Current score = -3324.6776 Performing final optimizations... -pass 1 : -3321.1625 (branch= 0.0809 alpha= 0.0053 pinv= 0.0162 eq freqs= 0.0760 rel rates= 0.6741 ins/del rates= 1.3641) -pass 2 : -3320.4671 (branch= 0.1141 alpha= 0.0000 pinv= 0.0300 eq freqs= 0.0144 rel rates= 0.5069 ins/del rates= 0.0299) -pass 3 : -3319.9579 (branch= 0.0614 alpha= 0.0048 pinv= 0.0162 eq freqs= 0.0150 rel rates= 0.3871 ins/del rates= 0.0246) -pass 4 : -3319.5645 (branch= 0.0361 alpha= 0.0091 pinv= 0.0153 eq freqs= 0.0039 rel rates= 0.3142 ins/del rates= 0.0147) -pass 5 : -3319.2468 (branch= 0.0239 alpha= 0.0102 pinv= 0.0145 eq freqs= 0.0021 rel rates= 0.2576 ins/del rates= 0.0094) -pass 6 : -3318.9921 (branch= 0.0149 alpha= 0.0098 pinv= 0.0140 eq freqs= 0.0008 rel rates= 0.2091 ins/del rates= 0.0061) -pass 7 : -3318.7934 (branch= 0.0094 alpha= 0.0104 pinv= 0.0131 eq freqs= 0.0008 rel rates= 0.1612 ins/del rates= 0.0039) -pass 8 : -3318.6302 (branch= 0.0060 alpha= 0.0102 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.1315 ins/del rates= 0.0026) -pass 9 : -3318.4984 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0004 rel rates= 0.1045 ins/del rates= 0.0017) -pass 10: -3318.3897 (branch= 0.0026 alpha= 0.0095 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0841 ins/del rates= 0.0011) -pass 11: -3318.3003 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0681 ins/del rates= 0.0008) -pass 12: -3318.2263 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0002 rel rates= 0.0550 ins/del rates= 0.0005) -pass 13: -3318.1643 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0450 ins/del rates= 0.0003) -pass 14: -3318.1116 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0002) -pass 15: -3318.0670 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0001) -pass 16: -3318.0292 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0254 ins/del rates= 0.0001) -pass 17: -3317.9966 (branch= 0.0001 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0215 ins/del rates= 0.0000) -pass 18: -3317.9685 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0182 ins/del rates= 0.0000) -pass 19: -3317.9442 (branch= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0155 ins/del rates= 0.0000) -pass 20: -3317.9231 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0132 ins/del rates= 0.0000) +pass 1 : -3321.6104 (branch= 0.8801 alpha= 0.0103 pinv= 0.0163 eq freqs= 0.0472 rel rates= 0.7957 ins/del rates= 1.3177) +pass 2 : -3320.5402 (branch= 0.3596 alpha= 0.0000 pinv= 0.0210 eq freqs= 0.0211 rel rates= 0.6304 ins/del rates= 0.0382) +pass 3 : -3319.9870 (branch= 0.0852 alpha= 0.0103 pinv= 0.0162 eq freqs= 0.0097 rel rates= 0.4088 ins/del rates= 0.0230) +pass 4 : -3319.5793 (branch= 0.0364 alpha= 0.0101 pinv= 0.0155 eq freqs= 0.0035 rel rates= 0.3294 ins/del rates= 0.0127) +pass 5 : -3319.2608 (branch= 0.0225 alpha= 0.0098 pinv= 0.0151 eq freqs= 0.0013 rel rates= 0.2606 ins/del rates= 0.0093) +pass 6 : -3319.0094 (branch= 0.0139 alpha= 0.0107 pinv= 0.0144 eq freqs= 0.0010 rel rates= 0.2056 ins/del rates= 0.0058) +pass 7 : -3318.8121 (branch= 0.0090 alpha= 0.0107 pinv= 0.0135 eq freqs= 0.0007 rel rates= 0.1595 ins/del rates= 0.0038) +pass 8 : -3318.6481 (branch= 0.0060 alpha= 0.0106 pinv= 0.0126 eq freqs= 0.0005 rel rates= 0.1319 ins/del rates= 0.0025) +pass 9 : -3318.5138 (branch= 0.0039 alpha= 0.0105 pinv= 0.0117 eq freqs= 0.0004 rel rates= 0.1062 ins/del rates= 0.0016) +pass 10: -3318.4029 (branch= 0.0025 alpha= 0.0100 pinv= 0.0115 eq freqs= 0.0004 rel rates= 0.0853 ins/del rates= 0.0011) +pass 11: -3318.3113 (branch= 0.0017 alpha= 0.0094 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0692 ins/del rates= 0.0007) +pass 12: -3318.2359 (branch= 0.0011 alpha= 0.0088 pinv= 0.0090 eq freqs= 0.0002 rel rates= 0.0558 ins/del rates= 0.0005) +pass 13: -3318.1728 (branch= 0.0008 alpha= 0.0081 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0455 ins/del rates= 0.0003) +pass 14: -3318.1191 (branch= 0.0005 alpha= 0.0075 pinv= 0.0075 eq freqs= 0.0001 rel rates= 0.0379 ins/del rates= 0.0002) +pass 15: -3318.0732 (branch= 0.0003 alpha= 0.0070 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0316 ins/del rates= 0.0001) +pass 16: -3318.0346 (branch= 0.0002 alpha= 0.0065 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0257 ins/del rates= 0.0001) +pass 17: -3318.0014 (branch= 0.0001 alpha= 0.0058 pinv= 0.0055 eq freqs= 0.0001 rel rates= 0.0216 ins/del rates= 0.0000) +pass 18: -3317.9727 (branch= 0.0001 alpha= 0.0052 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) +pass 19: -3317.9479 (branch= 0.0001 alpha= 0.0047 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0156 ins/del rates= 0.0000) +pass 20: -3317.9264 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0133 ins/del rates= 0.0000) optimization up to ... -pass 30: -3317.8190 (branch= 0.0001 alpha= 0.0217 pinv= 0.0200 eq freqs= 0.0001 rel rates= 0.0622 ins/del rates= 0.0000) +pass 30: -3317.8198 (branch= 0.0001 alpha= 0.0228 pinv= 0.0210 eq freqs= 0.0001 rel rates= 0.0625 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7943 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) +pass 40: -3317.7945 (branch= 0.0001 alpha= 0.0057 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) +pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0009 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0008 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 74: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 78: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 14 seconds +Final score = -3317.7870 +Time used so far = 0 hours, 0 minutes and 19 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.066, AG = 10.265, AT = 2.655, CG = 0.001, CT = 21.537, GT = 1.000 + AC = 3.066, AG = 10.270, AT = 2.658, CG = 0.001, CT = 21.546, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5751 + 0.5753 with an invariant (invariable) site category, proportion estimated - 0.3614 + 0.3615 Substitution rate categories under this model: rate proportion - 0.0000 0.3614 - 0.0480 0.1596 - 0.2981 0.1596 - 0.8680 0.1596 - 2.7858 0.1596 + 0.0000 0.3615 + 0.0481 0.1596 + 0.2983 0.1596 + 0.8682 0.1596 + 2.7855 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -14766,13 +14799,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.066 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 10.27 2.658 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -14906,14 +14939,6 @@ 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9460 0.010 1104 -2200 -210.8946 0.010 1104 -2400 -210.8863 0.010 1104 -2600 -210.8436 0.010 1104 -2800 -210.8250 0.010 1104 -3000 -210.8188 0.010 1104 -3200 -210.7905 0.010 1104 -3400 -210.7553 0.010 1104 -3600 -210.7287 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14993,37 +15018,46 @@ STARTING RUN Restarting from checkpoint... - generation 3766, seed 1263385291, best lnL -210.709 + generation 2051, seed 1461452574, best lnL -210.941 gen current_lnL precision last_tree_imp -3766 -210.7094 0.010 1104 -3800 -210.7083 0.010 1104 -3900 -210.7020 0.010 1104 -4000 -210.6946 0.010 1104 +2051 -210.9406 0.010 1104 +2100 -210.9365 0.010 1104 +2200 -210.8946 0.010 1104 +2300 -210.8921 0.010 1104 +2400 -210.8863 0.010 1104 +2500 -210.8674 0.010 1104 +2600 -210.8436 0.010 1104 +2700 -210.8339 0.010 1104 +2800 -210.8250 0.010 1104 +2900 -210.8228 0.010 1104 +3000 -210.8188 0.010 1104 +3100 -210.8049 0.010 1104 +3200 -210.7905 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.03869 +Improvement over last 500 gen = 0.04346 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.570, AG = 4.854, AT = 0.222, CG = 4.460, CT = 6.971, GT = 1.000 + AC = 2.253, AG = 4.316, AT = 0.229, CG = 3.799, CT = 6.513, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2329 0.3364 0.2106 0.2201 + (ACGT) 0.2299 0.3376 0.2132 0.2194 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.1902 + 1.1009 with an invariant (invariable) site category, proportion estimated - 0.1105 + 0.1054 Substitution rate categories under this model: rate proportion - 0.0000 0.1105 - 0.2293 0.2965 - 0.7543 0.2965 - 2.0164 0.2965 + 0.0000 0.1054 + 0.2110 0.2982 + 0.7362 0.2982 + 2.0528 0.2982 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -15031,11 +15065,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.6946 +Replicate 1 : -210.7905 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.57 4.854 0.2216 4.46 6.971 1 0.233 0.336 0.211 0.220 1.190 0.110 +rep 1: 2.253 4.316 0.2288 3.799 6.513 1 0.230 0.338 0.213 0.219 1.101 0.105 Treelengths: TL @@ -15170,17 +15204,6 @@ 1800 -166.8222 0.010 843 2000 -166.6788 0.010 843 2200 -166.5887 0.010 843 -2400 -166.4579 0.010 843 -2600 -166.3862 0.010 843 -2800 -166.3657 0.010 843 -3000 -166.3070 0.010 843 -3200 -166.2787 0.010 843 -3400 -166.2099 0.010 843 -3600 -166.0618 0.010 843 -3800 -165.9521 0.010 843 -4000 -165.9340 0.010 843 -4200 -165.8876 0.010 843 -4400 -165.8800 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15261,9 +15284,30 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 4471, seed 234127599, best lnL -165.855 +Bootstrap rep 1 (of 1) generation 2368, seed 2001893933, best lnL -166.459 gen current_lnL precision last_tree_imp -4471 -165.8546 0.010 843 +2368 -166.4594 0.010 843 +2400 -166.4579 0.010 843 +2500 -166.4472 0.010 843 +2600 -166.3862 0.010 843 +2700 -166.3767 0.010 843 +2800 -166.3657 0.010 843 +2900 -166.3552 0.010 843 +3000 -166.3070 0.010 843 +3100 -166.2830 0.010 843 +3200 -166.2787 0.010 843 +3300 -166.2763 0.010 843 +3400 -166.2099 0.010 843 +3500 -166.0931 0.010 843 +3600 -166.0618 0.010 843 +3700 -166.0204 0.010 843 +3800 -165.9521 0.010 843 +3900 -165.9405 0.010 843 +4000 -165.9340 0.010 843 +4100 -165.9078 0.010 843 +4200 -165.8876 0.010 843 +4300 -165.8812 0.010 843 +4400 -165.8800 0.010 843 4500 -165.8545 0.010 843 4600 -165.7809 0.010 843 4700 -165.7799 0.010 843 @@ -15286,54 +15330,30 @@ 6400 -165.1354 0.010 6021 6500 -165.1254 0.010 6021 6600 -165.0479 0.010 6021 -6700 -165.0438 0.010 6021 -6800 -165.0428 0.010 6021 -6900 -164.8438 0.010 6021 -7000 -164.8383 0.010 6021 -7100 -164.7890 0.010 6021 -7200 -164.6664 0.010 6021 -7300 -164.6617 0.010 6021 -7400 -164.6478 0.010 6021 -7500 -164.6472 0.010 6021 -7600 -164.5352 0.010 7573 -7700 -164.4035 0.010 7573 -7800 -164.3902 0.010 7573 -7900 -164.3595 0.010 7573 -8000 -164.3323 0.010 7573 -8100 -164.1711 0.010 7573 -8200 -164.1537 0.010 7573 -8300 -164.0538 0.010 7573 -8400 -164.0465 0.010 7573 -8500 -164.0049 0.010 7573 -8600 -163.9411 0.010 7573 -8700 -163.8406 0.010 7573 -8800 -163.8133 0.010 7573 -8900 -163.8024 0.010 7573 -9000 -163.7249 0.010 7573 NOTE: ****Specified time limit (5 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.785, AG = 10.958, AT = 2.211, CG = 4.183, CT = 36.394, GT = 1.000 + AC = 0.680, AG = 8.360, AT = 1.348, CG = 3.165, CT = 17.125, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1255 0.4233 0.2365 0.2147 + (ACGT) 0.1302 0.4096 0.2306 0.2295 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 3.0988 + 2.2195 with an invariant (invariable) site category, proportion estimated - 0.3385 + 0.3118 Substitution rate categories under this model: rate proportion - 0.0000 0.3385 - 0.3968 0.1654 - 0.7369 0.1654 - 1.0830 0.1654 - 1.7834 0.1654 + 0.0000 0.3118 + 0.3181 0.1720 + 0.6765 0.1720 + 1.0746 0.1720 + 1.9308 0.1720 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 2 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) <<< @@ -15345,15 +15365,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -163.7242 (TERMINATED PREMATURELY) +Replicate 1 : -165.0462 (TERMINATED PREMATURELY) Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.7848 10.96 2.211 4.183 36.39 1 0.126 0.423 0.236 0.215 3.099 0.338 +rep 1: 0.6803 8.36 1.348 3.165 17.12 1 0.130 0.410 0.231 0.229 2.219 0.312 Treelengths: TL -rep 1: 3.159 +rep 1: 2.321 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -15494,7 +15514,6 @@ 6800 -212.7057 0.010 3769 7000 -212.7025 0.010 3769 7200 -212.7020 0.010 3769 -7400 -212.6750 0.010 3769 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15574,21 +15593,21 @@ STARTING RUN Restarting from checkpoint... - generation 7598, seed 440755700, best lnL -212.670 + generation 7360, seed 1881187052, best lnL -212.675 gen current_lnL precision last_tree_imp -7598 -212.6702 0.010 3769 -7600 -212.6702 0.010 3769 +7360 -212.6750 0.010 3769 +7400 -212.6750 0.010 3769 Reached termination condition! last topological improvement at gen 3769 -Improvement over last 500 gen = 0.03227 +Improvement over last 500 gen = 0.02846 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.420, AG = 10.376, AT = 0.430, CG = 10.468, CT = 6.838, GT = 1.000 + AC = 5.420, AG = 10.239, AT = 0.430, CG = 10.468, CT = 6.648, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2205 0.2887 0.1831 0.3078 + (ACGT) 0.2195 0.2891 0.1833 0.3081 Rate Heterogeneity Model: no rate heterogeneity @@ -15601,15 +15620,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.6702 +Replicate 1 : -212.6750 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 5.42 10.38 0.4295 10.47 6.838 1 0.220 0.289 0.183 0.308 +rep 1: 5.42 10.24 0.4295 10.47 6.648 1 0.220 0.289 0.183 0.308 Treelengths: TL -rep 1: 1.728 +rep 1: 1.729 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -15757,7 +15776,6 @@ 4600 -210.6208 0.010 2883 4800 -210.5769 0.010 2883 5000 -210.5647 0.010 2883 -5200 -210.5368 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15845,9 +15863,12 @@ STARTING RUN Restarting from checkpoint... - generation 5329, seed 612164611, best lnL -210.512 + generation 5040, seed 579689416, best lnL -210.563 gen current_lnL precision last_tree_imp -5329 -210.5122 0.010 2883 +5040 -210.5632 0.010 2883 +5100 -210.5566 0.010 2883 +5200 -210.5368 0.010 2883 +5300 -210.5127 0.010 2883 5400 -210.5093 0.010 2883 5500 -210.5012 0.010 2883 5600 -210.4832 0.010 2883 @@ -16106,10 +16127,6 @@ 200 -13373.8435 0.500 0 300 -13372.9677 0.500 0 400 -13371.8985 0.500 0 -500 -13371.5864 0.500 0 -Optimization precision reduced - Optimizing parameters... improved 0.048 lnL - Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16232,12 +16249,15 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 532, seed 1053527202, best lnL -13371.442 +Bootstrap rep 1 (of 1) generation 492, seed 1942976702, best lnL -13371.665 gen current_lnL precision last_tree_imp -532 -13371.4417 0.402 0 +492 -13371.6655 0.500 0 +500 -13371.5864 0.500 0 +Optimization precision reduced + Optimizing parameters... improved 0.048 lnL + Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -13371.0754 0.402 0 -800 -13370.9489 0.402 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16245,7 +16265,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.413, AG = 2.328, AT = 1.077, CG = 1.077, CT = 3.707, GT = 1.000 + AC = 1.413, AG = 2.288, AT = 1.077, CG = 1.077, CT = 3.707, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3111 0.1852 0.3053 0.1984 Rate Heterogeneity Model: @@ -16264,7 +16284,7 @@ User specified matrix type: ( 0 1 2 1 0 3 ) AC = 2.627, AG = 4.236, AT = 0.821, CG = 4.236, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2812 0.1777 0.1599 0.3811 + (ACGT) 0.2817 0.1763 0.1602 0.3818 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2463 @@ -16310,25 +16330,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.9488 (TERMINATED PREMATURELY) +Replicate 1 : -13370.9606 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.413 2.328 1.077 1.077 3.707 1 0.311 0.185 0.305 0.198 0.353 +rep 1: 1.413 2.288 1.077 1.077 3.707 1 0.311 0.185 0.305 0.198 0.353 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.627 4.236 0.8209 4.236 2.627 1 0.281 0.178 0.160 0.381 0.246 +rep 1: 2.627 4.236 0.8209 4.236 2.627 1 0.282 0.176 0.160 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.382 4.42 0.6343 5.382 1 0.155 0.345 0.278 0.222 4.109 0.047 +rep 1: 1 5.382 4.42 0.6342 5.382 1 0.155 0.345 0.278 0.222 4.109 0.047 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.772 0.530 0.285 2.185 +rep 1: 1.771 0.530 0.285 2.185 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16528,6 +16548,7 @@ 3200 -467.7183 0.010 76 3300 -467.7165 0.010 76 3400 -467.7165 0.010 76 +3500 -467.7162 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16653,10 +16674,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3461, seed 271493482, best lnL -467.716 +Search rep 1 (of 5) generation 3564, seed 1166954729, best lnL -467.716 gen current_lnL precision last_tree_imp -3461 -467.7164 0.010 76 -3500 -467.7162 0.010 76 +3564 -467.7160 0.010 76 3600 -467.7160 0.010 76 3700 -467.7160 0.010 76 3800 -467.7159 0.010 76 @@ -17264,6 +17284,7 @@ lnL after optimization: -477.8527 gen current_lnL precision last_tree_imp 0 -477.8527 0.010 0 +100 -477.7879 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17389,10 +17410,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1, seed 1140057502, best lnL -477.853 +Search rep 2 (of 5) generation 199, seed 1643364741, best lnL -477.766 gen current_lnL precision last_tree_imp -1 -477.8527 0.010 0 -100 -477.7879 0.010 74 +199 -477.7665 0.010 74 200 -477.7665 0.010 74 300 -477.7486 0.010 74 400 -477.7424 0.010 74 @@ -17425,24 +17445,26 @@ 3100 -477.3140 0.010 2170 3200 -477.3125 0.010 2170 3300 -477.3125 0.010 2170 +3400 -477.3123 0.010 2170 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.3125 +Current score = -477.3116 Performing final optimizations... -pass 1 : -477.2438 (branch= 0.0000 subset rates= 0.0687) -pass 2 : -477.2269 (branch= 0.0113 subset rates= 0.0056) -pass 3 : -477.2182 (branch= 0.0087 subset rates= 0.0000) -pass 4 : -477.2113 (branch= 0.0069 subset rates= 0.0000) -pass 5 : -477.2078 (branch= 0.0035 subset rates= 0.0000) -pass 6 : -477.2064 (branch= 0.0009 subset rates= 0.0005) -pass 7 : -477.2052 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -477.2046 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -477.2045 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2044 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2044 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2044 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2393 (branch= 0.0000 subset rates= 0.0723) +pass 2 : -477.2289 (branch= 0.0086 subset rates= 0.0018) +pass 3 : -477.2162 (branch= 0.0125 subset rates= 0.0002) +pass 4 : -477.2102 (branch= 0.0060 subset rates= 0.0000) +pass 5 : -477.2077 (branch= 0.0025 subset rates= 0.0000) +pass 6 : -477.2066 (branch= 0.0011 subset rates= 0.0000) +pass 7 : -477.2052 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -477.2048 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -477.2046 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2046 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.2045 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2043 +Final score = -477.2045 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17489,7 +17511,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.4316 -Replicate 2 : -477.2043 (best) (TERMINATED PREMATURELY) +Replicate 2 : -477.2045 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17505,7 +17527,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.917 2.740 -rep 2: 4.699 0.634 1.939 2.635 +rep 2: 4.699 0.633 1.942 2.630 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### @@ -17703,7 +17725,6 @@ 2800 -425.5890 0.010 365 2900 -425.5876 0.010 365 3000 -425.5875 0.010 365 -3100 -425.5854 0.010 365 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17832,9 +17853,10 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3102, seed 169259964, best lnL -425.585 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3054, seed 1091748661, best lnL -425.587 gen current_lnL precision last_tree_imp -3102 -425.5854 0.010 365 +3054 -425.5870 0.010 365 +3100 -425.5854 0.010 365 3200 -425.5852 0.010 365 3300 -425.5851 0.010 365 3400 -425.5828 0.010 365 @@ -17935,25 +17957,27 @@ 2200 -425.5912 0.010 523 2300 -425.5897 0.010 523 2400 -425.5887 0.010 523 +2500 -425.5882 0.010 523 +2600 -425.5881 0.010 523 +2700 -425.5867 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.5885 +Current score = -425.5863 Performing final optimizations... -pass 1 : -425.5777 (branch= 0.0000 subset rates= 0.0108) -pass 2 : -425.5573 (branch= 0.0204 subset rates= 0.0000) -pass 3 : -425.5560 (branch= 0.0013 subset rates= 0.0000) -pass 4 : -425.5517 (branch= 0.0043 subset rates= 0.0000) -pass 5 : -425.5512 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -425.5503 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -425.5495 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.5489 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.5489 (branch= 0.0000 subset rates= 0.0000) -pass 11: -425.5488 (branch= 0.0001 subset rates= 0.0000) -pass 12: -425.5488 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5488 (branch= 0.0000 subset rates= 0.0000) -pass 14: -425.5488 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.5776 (branch= 0.0000 subset rates= 0.0087) +pass 2 : -425.5564 (branch= 0.0196 subset rates= 0.0016) +pass 3 : -425.5551 (branch= 0.0013 subset rates= 0.0000) +pass 4 : -425.5526 (branch= 0.0025 subset rates= 0.0000) +pass 5 : -425.5513 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -425.5503 (branch= 0.0010 subset rates= 0.0000) +pass 7 : -425.5500 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -425.5495 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -425.5492 (branch= 0.0001 subset rates= 0.0001) +pass 10: -425.5491 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5488 (branch= 0.0000 subset rates= 0.0003) +pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5488 +Final score = -425.5487 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17982,9 +18006,9 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.52 1.12 + 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 10 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< @@ -18000,7 +18024,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5488 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -425.5487 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18016,7 +18040,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.037 0.868 1.530 1.116 -rep 2: 3.039 0.869 1.525 1.119 +rep 2: 3.037 0.867 1.534 1.122 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -18208,6 +18232,7 @@ 2300 -473.9814 0.010 653 2400 -473.9804 0.010 653 2500 -473.9804 0.010 653 +2600 -473.9801 0.010 653 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18333,10 +18358,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2500, seed 988000168, best lnL -473.980 +Search rep 1 (of 5) generation 2610, seed 1349867826, best lnL -473.980 gen current_lnL precision last_tree_imp -2500 -473.9804 0.010 653 -2600 -473.9801 0.010 653 +2610 -473.9801 0.010 653 2700 -473.9793 0.010 653 2800 -473.9779 0.010 653 2900 -473.9777 0.010 653 @@ -18364,7 +18388,7 @@ pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 12 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18448,27 +18472,41 @@ 500 -474.5075 0.010 272 600 -474.5034 0.010 272 700 -474.4997 0.010 272 +800 -474.4937 0.010 272 +900 -474.4913 0.010 272 +1000 -474.4880 0.010 272 +1100 -474.4855 0.010 272 +1200 -474.4847 0.010 272 +1300 -474.4838 0.010 272 +1400 -474.4822 0.010 272 +1500 -474.4804 0.010 272 +1600 -474.4798 0.010 272 +1700 -474.4795 0.010 272 +1800 -474.4790 0.010 272 +1900 -474.4786 0.010 272 +2000 -474.4786 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4967 +Current score = -474.4786 Performing final optimizations... -pass 1 : -474.4798 (branch= 0.0169 subset rates= 0.0000) -pass 2 : -474.4499 (branch= 0.0299 subset rates= 0.0000) -pass 3 : -474.4433 (branch= 0.0066 subset rates= 0.0000) -pass 4 : -474.4354 (branch= 0.0077 subset rates= 0.0002) -pass 5 : -474.4316 (branch= 0.0038 subset rates= 0.0000) -pass 6 : -474.4307 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -474.4301 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -474.4294 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -474.4289 (branch= 0.0005 subset rates= 0.0000) -pass 10: -474.4287 (branch= 0.0002 subset rates= 0.0000) -pass 11: -474.4286 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4286 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.4285 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.4285 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4285 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4638 (branch= 0.0148 subset rates= 0.0000) +pass 2 : -474.4449 (branch= 0.0189 subset rates= 0.0000) +pass 3 : -474.4417 (branch= 0.0032 subset rates= 0.0000) +pass 4 : -474.4356 (branch= 0.0061 subset rates= 0.0000) +pass 5 : -474.4342 (branch= 0.0014 subset rates= 0.0000) +pass 6 : -474.4317 (branch= 0.0026 subset rates= 0.0000) +pass 7 : -474.4302 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -474.4298 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -474.4292 (branch= 0.0004 subset rates= 0.0002) +pass 10: -474.4290 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0001 subset rates= 0.0006) +pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 16: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4285 -Time used so far = 0 hours, 0 minutes and 14 seconds +Final score = -474.4281 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -18496,7 +18534,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.91 + 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -18514,7 +18552,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9507 (best) -Replicate 2 : -474.4285 (TERMINATED PREMATURELY) +Replicate 2 : -474.4281 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18530,7 +18568,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.066 2.804 -rep 2: 4.597 0.589 2.028 2.912 +rep 2: 4.600 0.588 2.032 2.919 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -18548,13 +18586,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j3 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' - /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -18594,10 +18632,10 @@ dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect +dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged @@ -18607,9 +18645,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_armhf.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_armhf.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_armhf.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_armhf.buildinfo @@ -18619,12 +18657,14 @@ 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/4131/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4131/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/32626 and its subdirectories -I: Current time: Sat Jan 11 17:53:57 -12 2025 -I: pbuilder-time-stamp: 1736661237 +I: removing directory /srv/workspace/pbuilder/4131 and its subdirectories +I: Current time: Sun Jan 12 20:28:06 +14 2025 +I: pbuilder-time-stamp: 1736663286