Diff of the two buildlogs: -- --- b1/build.log 2025-08-26 11:27:55.814442637 +0000 +++ b2/build.log 2025-08-26 11:33:57.174867679 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 25 23:23:43 -12 2025 -I: pbuilder-time-stamp: 1756207423 +I: Current time: Tue Sep 29 07:50:57 +14 2026 +I: pbuilder-time-stamp: 1790617857 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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/3262707/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1370477/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 28 17:51 /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/1370477/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1370477/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f32df1f606ae457b801d1e07ef81ef90' - 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='3262707' - PS1='# ' - PS2='> ' + INVOCATION_ID=9401c292f6b348ddabcc4f16eaf59e8a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=1370477 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.c3PgVwTI/pbuilderrc_qXC0 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.c3PgVwTI/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.c3PgVwTI/pbuilderrc_yq1h --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.c3PgVwTI/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.41+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3262707/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1370477/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -217,7 +249,7 @@ Get: 104 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.7-1 [1089 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 106 http://deb.debian.org/debian forky/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] -Fetched 101 MB in 1s (71.2 MB/s) +Fetched 101 MB in 1s (83.8 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 ... 19855 files and directories currently installed.) @@ -664,7 +696,11 @@ 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/1370477/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1370477/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 @@ -769,8 +805,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... 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 @@ -839,7 +875,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j12 + make -j16 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -857,16 +893,64 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ +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; + | ^~~ +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{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from bipartition.h:23, + from bipartition.cpp:19: +/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) + | ^~~~~~~ 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, @@ -889,13 +973,78 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from bipartition.cpp:20: +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from configreader.cpp:30: 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 bipartition.h:23, - from bipartition.cpp:19: + 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 configreader.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) + | ^~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.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 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 population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -933,6 +1082,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from garlimain.cpp:46: +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{ | ^~~~~~~~~~~~~~~ -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 population.h:23: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1001,6 +1149,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from optimization.cpp:21: +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 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) - | ^~~~~~~ -In file included from garlimain.cpp:46: -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 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{ | ^~~~~~~~~~~~~~~ @@ -1126,7 +1274,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1157,7 +1305,6 @@ /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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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; @@ -1165,21 +1312,23 @@ /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{ | ^~~~~~~~~~~~~~~ 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 population.h:23: + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1217,10 +1366,15 @@ /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{ | ^~~~~~~~~~~~~~~ -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/iomanip:42, - from individual.cpp:21: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1275,15 +1426,46 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from population.cpp:49: 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{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.h:24: +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 | ^~~~~~~~~~~~~~~ @@ -1432,22 +1583,17 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from optimization.cpp:21: -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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1485,7 +1631,10 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from population.cpp:49: +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: + 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 model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1589,13 +1812,7 @@ 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 datamatr.cpp:20: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1652,12 +1869,14 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.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/string:54, + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1669,20 +1888,13 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.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 rng.h:36, - from tree.h:30: + from translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1694,98 +1906,49 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ +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 datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/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 'int SubGarliMain(int)' at garlimain.cpp:322:25: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from tree.cpp:33: -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/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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{ @@ -2269,27 +2325,12 @@ /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/x86_64-linux-gnu/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 ()); - | ~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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 tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from funcs.cpp:30: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2337,16 +2378,62 @@ /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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +In file included from garlimain.cpp:46: 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{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.h:24: +/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) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from configreader.cpp:30: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2356,7 +2443,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2394,19 +2481,23 @@ /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{ | ^~~~~~~~~~~~~~~ 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 model.cpp:17: + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2444,14 +2535,11 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -2499,11 +2587,16 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from optimization.cpp:21: +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{ | ^~~~~~~~~~~~~~~ @@ -2513,7 +2606,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2551,29 +2644,56 @@ /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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.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 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/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.cpp:17: +/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 + | ^~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from population.cpp:45: +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/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2604,6 +2724,28 @@ /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::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) + | ^~~~~~~ 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; @@ -2611,45 +2753,12 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from population.cpp:49: 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{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.h:24: -/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) - | ^~~~~~~ -In file included from optimization.cpp:21: -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{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2798,6 +2893,10 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': +reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 388 | fread(&unique, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)); @@ -2806,6 +2905,10 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +reconnode.h: In constructor 'Swap::Swap(FILE*&)': +reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 264 | fread(&count, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)); @@ -2813,27 +2916,6 @@ /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) - | ^~~~~~~ -In file included from population.cpp:49: -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 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) + | ^~~~~~~ population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1887 | fread((char *) &t, sizeof(t), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, 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 configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2892,8 +3064,9 @@ /usr/include/x86_64-linux-gnu/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/ncl/ncl.h:27, - from garlireader.cpp:41: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2922,7 +3095,10 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2971,13 +3147,18 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.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/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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2989,7 +3170,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +/usr/include/x86_64-linux-gnu/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, @@ -3006,19 +3187,14 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.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 rng.h:36, - from tree.h:30: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3030,66 +3206,13 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -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 -fcf-protection -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, - from funcs.h:25, - from tree.cpp:33: -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/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, 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 translatetable.h:24, - from translatetable.cpp:19: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3226,28 +3284,6 @@ 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/x86_64-linux-gnu/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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/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, from datamatr.h:23, from sequencedata.h:27, from tree.cpp:31: @@ -3278,7 +3314,7 @@ # 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 -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 + make -j16 check "TESTSUITEFLAGS=-j16 --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' @@ -6245,7 +6281,7 @@ 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 5 seconds +Time used = 0 hours, 0 minutes and 9 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6397,7 +6433,7 @@ 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 4 seconds +Time used = 0 hours, 0 minutes and 6 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6601,7 +6637,7 @@ pass 80: -3350.2336 (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 = -3350.2336 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6809,7 +6845,7 @@ pass 76: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7294,7 +7330,7 @@ pass 16: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9518,7 +9554,7 @@ pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9782,7 +9818,7 @@ 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 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10363,7 +10399,7 @@ pass 490: -208.3575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) Looking for minimum length branches... Final score = -208.3575 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13094,61 +13130,15 @@ 2200 -88.6224 0.010 879 2300 -88.6154 0.010 879 2400 -88.6058 0.010 879 -2500 -88.5913 0.010 879 -2600 -88.5622 0.010 879 -2700 -88.5467 0.010 879 -2800 -88.5396 0.010 879 -2900 -88.5337 0.010 879 -3000 -88.5266 0.010 879 -3100 -88.5249 0.010 879 -Reached termination condition! -last topological improvement at gen 879 -Improvement over last 500 gen = 0.03733 - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 20 (amino acid data) - Amino Acid Rate Matrix: Jones - Equilibrium State Frequencies: empirical (observed) values (+F) - (ACDEFGHIKLMNPQRSTVWY) - 0.0165 0.0083 0.0496 0.0909 0.0909 - 0.0083 0.0744 0.0083 0.0083 0.1074 - 0.1157 0.0248 0.1240 0.0331 0.0083 - 0.0826 0.0496 0.0579 0.0083 0.0331 - Rate Heterogeneity Model: - 3 discrete gamma distributed rate categories, alpha param estimated - 3.1527 - with an invariant (invariable) site category, proportion estimated - 0.2947 - Substitution rate categories under this model: - rate proportion - 0.0000 0.2947 - 0.4599 0.2351 - 0.9028 0.2351 - 1.6373 0.2351 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -88.5249 - -Parameter estimates: - alpha pinv -rep 1: 3.153 0.295 - -Treelengths: - TL -rep 1: 2.365 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.a.G3.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. ->>>Completed Bootstrap rep 1<<< -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -13236,9 +13226,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3100, seed 1872184071, best lnL -88.525 +Bootstrap rep 1 (of 1) generation 2436, seed 1717032462, best lnL -88.593 gen current_lnL precision last_tree_imp -3100 -88.5249 0.010 879 +2436 -88.5926 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13252,15 +13242,15 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 3.1527 + 2.1428 with an invariant (invariable) site category, proportion estimated - 0.2947 + 0.2575 Substitution rate categories under this model: rate proportion - 0.0000 0.2947 - 0.4599 0.2351 - 0.9028 0.2351 - 1.6373 0.2351 + 0.0000 0.2575 + 0.3708 0.2475 + 0.8587 0.2475 + 1.7705 0.2475 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. @@ -13270,15 +13260,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.5249 +Replicate 1 : -88.5926 Parameter estimates: alpha pinv -rep 1: 3.153 0.295 +rep 1: 2.143 0.257 Treelengths: TL -rep 1: 2.365 +rep 1: 2.411 Saving best tree to bootstrap file ch.a.G3.boot.tre @@ -13419,12 +13409,6 @@ 1400 -110.3747 0.010 707 1500 -110.3652 0.010 707 1600 -110.2968 0.010 707 -1700 -110.2780 0.010 707 -1800 -110.2330 0.010 707 -1900 -110.2137 0.010 707 -2000 -110.1885 0.010 707 -2100 -110.1532 0.010 707 -2200 -110.1459 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13511,9 +13495,9 @@ STARTING RUN Restarting from checkpoint... - generation 2283, seed 1253314916, best lnL -110.135 + generation 1621, seed 182002031, best lnL -110.286 gen current_lnL precision last_tree_imp -2283 -110.1348 0.010 707 +1621 -110.2862 0.010 707 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13527,16 +13511,16 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 3.5915 + 2.1759 with an invariant (invariable) site category, proportion estimated - 0.1847 + 0.1446 Substitution rate categories under this model: rate proportion - 0.0000 0.1847 - 0.4304 0.2038 - 0.7598 0.2038 - 1.0842 0.2038 - 1.7256 0.2038 + 0.0000 0.1446 + 0.3134 0.2138 + 0.6725 0.2138 + 1.0738 0.2138 + 1.9403 0.2138 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -13547,15 +13531,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -110.1348 +Replicate 1 : -110.2862 Parameter estimates: alpha pinv -rep 1: 3.591 0.185 +rep 1: 2.176 0.145 Treelengths: TL -rep 1: 2.701 +rep 1: 2.679 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log @@ -13995,23 +13979,6 @@ 140 -205.2440 0.500 121 150 -205.1047 0.500 121 160 -205.0609 0.500 121 -170 -204.9812 0.500 121 -180 -204.9247 0.500 172 -190 -204.8909 0.500 172 -200 -204.7980 0.500 172 -210 -204.7143 0.500 209 -220 -204.6664 0.500 209 -230 -204.3372 0.500 228 -240 -204.3152 0.500 228 -250 -203.9441 0.500 245 -260 -203.9053 0.500 245 -270 -203.8090 0.500 245 -280 -203.8090 0.500 245 -290 -203.7595 0.500 245 -300 -203.7386 0.500 245 -310 -203.7108 0.500 245 -320 -203.5911 0.500 245 -330 -203.5298 0.500 245 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14098,15 +14065,15 @@ STARTING RUN Restarting from checkpoint... - generation 336, seed 2082909731, best lnL -203.514 + generation 160, seed 375495465, best lnL -205.061 gen current_lnL precision last_tree_imp -336 -203.5136 0.500 245 +160 -205.0609 0.500 121 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.696, AG = 4.221, AT = 0.041, CG = 2.532, CT = 4.060, GT = 1.000 + AC = 1.586, AG = 4.036, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14127,8 +14094,8 @@ 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion - 0.0473 0.5118 - 0.4995 0.4882 + 0.0473 0.5211 + 0.4995 0.4789 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -14139,15 +14106,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -203.5136 +Replicate 1 : -205.0609 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.047 0.512 0.499 0.488 1.696 4.221 0.04129 2.532 4.06 1 +rep 1: 0.047 0.521 0.499 0.479 1.586 4.036 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 8.188 +rep 1: 7.757 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log @@ -14290,27 +14257,6 @@ 110 -194.8986 0.500 0 120 -194.8986 0.500 0 130 -194.8984 0.500 0 -140 -194.8500 0.500 0 -150 -194.7085 0.500 0 -160 -194.7085 0.500 0 -170 -194.5936 0.500 168 -180 -194.5926 0.500 168 -190 -194.5693 0.500 168 -200 -194.2413 0.500 196 -210 -194.2413 0.500 196 -220 -194.2043 0.500 196 -230 -194.1525 0.500 196 -240 -194.0255 0.500 234 -250 -194.0104 0.500 234 -260 -193.9860 0.500 234 -270 -193.8167 0.500 234 -280 -193.8167 0.500 234 -290 -193.7620 0.500 234 -300 -193.7592 0.500 234 -310 -193.7487 0.500 234 -320 -193.6856 0.500 234 -330 -193.3200 0.500 324 -340 -193.2196 0.500 324 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14398,16 +14344,16 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 349, seed 1668018871, best lnL -193.219 +Bootstrap rep 1 (of 1) generation 135, seed 1001481219, best lnL -194.898 gen current_lnL precision last_tree_imp -349 -193.2193 0.500 324 +135 -194.8984 0.500 0 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.745, AG = 6.152, AT = 0.012, CG = 4.367, CT = 2.255, GT = 1.000 + AC = 1.637, AG = 5.750, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14435,15 +14381,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -193.2193 +Replicate 1 : -194.8984 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.745 6.152 0.01199 4.367 2.255 1 +rep 1: 0.121 1.000 1.637 5.75 0.01146 4.174 2.324 1 Treelengths: TL -rep 1: 8.209 +rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre @@ -14629,31 +14575,6 @@ 2900 -3351.0137 0.010 0 3000 -3351.0137 0.010 0 3100 -3351.0009 0.010 0 -3200 -3350.9813 0.010 0 -3300 -3350.9788 0.010 0 -3400 -3350.9754 0.010 0 -3500 -3350.9753 0.010 0 -3600 -3350.9747 0.010 0 -3700 -3350.9418 0.010 0 -3800 -3350.9275 0.010 0 -3900 -3350.8675 0.010 0 -4000 -3350.8675 0.010 0 -4100 -3350.8578 0.010 0 -4200 -3350.8523 0.010 0 -4300 -3350.8521 0.010 0 -4400 -3350.8480 0.010 0 -4500 -3350.8480 0.010 0 -4600 -3350.8168 0.010 0 -4700 -3350.8148 0.010 0 -4800 -3350.8148 0.010 0 -4900 -3350.8148 0.010 0 -5000 -3350.8140 0.010 0 -5100 -3350.7921 0.010 0 -5200 -3350.7743 0.010 0 -5300 -3350.7724 0.010 0 -5400 -3350.7562 0.010 0 -5500 -3350.7006 0.010 0 -5600 -3350.6580 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14757,89 +14678,66 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 5605, seed 141273333, best lnL -3350.658 +Search rep 1 (of 2) generation 3100, seed 276541511, best lnL -3351.001 gen current_lnL precision last_tree_imp -5605 -3350.6580 0.010 0 +3100 -3351.0009 0.010 0 +3200 -3350.9813 0.010 0 +3300 -3350.9788 0.010 0 +3400 -3350.9754 0.010 0 +3500 -3350.9753 0.010 0 +3600 -3350.9747 0.010 0 +3700 -3350.9418 0.010 0 +3800 -3350.9275 0.010 0 +3900 -3350.8675 0.010 0 +4000 -3350.8675 0.010 0 +4100 -3350.8578 0.010 0 +4200 -3350.8523 0.010 0 +4300 -3350.8521 0.010 0 +4400 -3350.8480 0.010 0 +4500 -3350.8480 0.010 0 +4600 -3350.8168 0.010 0 +4700 -3350.8148 0.010 0 +4800 -3350.8148 0.010 0 +4900 -3350.8148 0.010 0 +5000 -3350.8140 0.010 0 +5100 -3350.7921 0.010 0 +5200 -3350.7743 0.010 0 +5300 -3350.7724 0.010 0 +5400 -3350.7562 0.010 0 +5500 -3350.7006 0.010 0 +5600 -3350.6580 0.010 0 5700 -3350.6554 0.010 0 -5800 -3350.6195 0.010 0 -5900 -3350.6124 0.010 0 -6000 -3350.6088 0.010 0 -6100 -3350.5997 0.010 0 -6200 -3350.5989 0.010 0 -6300 -3350.5944 0.010 0 -6400 -3350.5915 0.010 0 -6500 -3350.5909 0.010 0 -6600 -3350.5895 0.010 0 -6700 -3350.5895 0.010 0 -6800 -3350.5827 0.010 0 -6900 -3350.5549 0.010 0 -7000 -3350.5549 0.010 0 -7100 -3350.5524 0.010 0 -7200 -3350.5463 0.010 0 -7300 -3350.5463 0.010 0 -7400 -3350.5431 0.010 0 -7500 -3350.5408 0.010 0 -7600 -3350.5321 0.010 0 -7700 -3350.5313 0.010 0 -7800 -3350.5313 0.010 0 -7900 -3350.5313 0.010 0 -8000 -3350.5125 0.010 0 -8100 -3350.5125 0.010 0 -8200 -3350.5124 0.010 0 -8300 -3350.5091 0.010 0 -8400 -3350.5003 0.010 0 -8500 -3350.4986 0.010 0 -8600 -3350.4798 0.010 0 -8700 -3350.4787 0.010 0 -8800 -3350.4784 0.010 0 -8900 -3350.4761 0.010 0 -9000 -3350.4758 0.010 0 -9100 -3350.4501 0.010 0 -9200 -3350.4501 0.010 0 -9300 -3350.4501 0.010 0 -9400 -3350.4495 0.010 0 -9500 -3350.4492 0.010 0 -9600 -3350.4482 0.010 0 -9700 -3350.4481 0.010 0 -9800 -3350.4481 0.010 0 -9900 -3350.4481 0.010 0 -10000 -3350.4473 0.010 0 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -10100 -3350.4468 0.010 0 -10200 -3350.4465 0.010 0 -10300 -3350.4462 0.010 0 -10400 -3350.4462 0.010 0 -10500 -3350.4461 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.4461 +Current score = -3350.6228 Performing final optimizations... -pass 1 : -3350.4354 (branch= 0.0000 alpha= 0.0000 pinv= 0.0107 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 2 : -3350.4128 (branch= 0.0000 alpha= 0.0121 pinv= 0.0104 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 3 : -3350.3874 (branch= 0.0000 alpha= 0.0108 pinv= 0.0093 eq freqs= 0.0000 rel rates= 0.0052 subset rates= 0.0000) -pass 4 : -3350.3693 (branch= 0.0018 alpha= 0.0076 pinv= 0.0086 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 5 : -3350.3532 (branch= 0.0000 alpha= 0.0086 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 6 : -3350.3378 (branch= 0.0007 alpha= 0.0077 pinv= 0.0067 eq freqs= 0.0002 rel rates= 0.0000 subset rates= 0.0000) -pass 7 : -3350.3246 (branch= 0.0007 alpha= 0.0065 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 8 : -3350.3131 (branch= 0.0001 alpha= 0.0060 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 9 : -3350.3029 (branch= 0.0001 alpha= 0.0054 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 10: -3350.2938 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 11: -3350.2859 (branch= 0.0000 alpha= 0.0042 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 12: -3350.2780 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0010) -pass 13: -3350.2716 (branch= 0.0005 alpha= 0.0030 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 14: -3350.2665 (branch= 0.0001 alpha= 0.0025 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 15: -3350.2619 (branch= 0.0000 alpha= 0.0024 pinv= 0.0022 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 16: -3350.2579 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 17: -3350.2544 (branch= 0.0000 alpha= 0.0019 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 18: -3350.2513 (branch= 0.0000 alpha= 0.0016 pinv= 0.0014 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 19: -3350.2487 (branch= 0.0000 alpha= 0.0014 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 20: -3350.2464 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 1 : -3350.6005 (branch= 0.0000 alpha= 0.0000 pinv= 0.0099 eq freqs= 0.0001 rel rates= 0.0092 subset rates= 0.0032) +pass 2 : -3350.5534 (branch= 0.0093 alpha= 0.0168 pinv= 0.0140 eq freqs= 0.0026 rel rates= 0.0029 subset rates= 0.0015) +pass 3 : -3350.5143 (branch= 0.0044 alpha= 0.0141 pinv= 0.0133 eq freqs= 0.0027 rel rates= 0.0047 subset rates= 0.0000) +pass 4 : -3350.4819 (branch= 0.0044 alpha= 0.0132 pinv= 0.0124 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) +pass 5 : -3350.4518 (branch= 0.0023 alpha= 0.0119 pinv= 0.0110 eq freqs= 0.0000 rel rates= 0.0030 subset rates= 0.0019) +pass 6 : -3350.4262 (branch= 0.0031 alpha= 0.0100 pinv= 0.0101 eq freqs= 0.0000 rel rates= 0.0025 subset rates= 0.0000) +pass 7 : -3350.4024 (branch= 0.0009 alpha= 0.0093 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0017) +pass 8 : -3350.3818 (branch= 0.0019 alpha= 0.0084 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0020 subset rates= 0.0000) +pass 9 : -3350.3644 (branch= 0.0003 alpha= 0.0076 pinv= 0.0073 eq freqs= 0.0000 rel rates= 0.0022 subset rates= 0.0000) +pass 10: -3350.3473 (branch= 0.0001 alpha= 0.0072 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0021 subset rates= 0.0012) +pass 11: -3350.3330 (branch= 0.0007 alpha= 0.0062 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0016 subset rates= 0.0000) +pass 12: -3350.3206 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0016 subset rates= 0.0000) +pass 13: -3350.3094 (branch= 0.0000 alpha= 0.0051 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0015 subset rates= 0.0000) +pass 14: -3350.2995 (branch= 0.0000 alpha= 0.0046 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0013 subset rates= 0.0000) +pass 15: -3350.2907 (branch= 0.0000 alpha= 0.0040 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0012 subset rates= 0.0000) +pass 16: -3350.2829 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 17: -3350.2762 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 18: -3350.2703 (branch= 0.0000 alpha= 0.0027 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) +pass 19: -3350.2651 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) +pass 20: -3350.2606 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2386 (branch= 0.0000 alpha= 0.0102 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) optimization up to ... -pass 30: -3350.2355 (branch= 0.0000 alpha= 0.0057 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 40: -3350.2341 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2333 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 50: -3350.2331 (branch= 0.0000 alpha= 0.0004 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2330 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 57: -3350.2330 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2330 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -14848,21 +14746,21 @@ Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.147, AG = 10.527, AT = 2.722, CG = 0.001, CT = 22.184, GT = 1.000 + AC = 3.121, AG = 10.439, AT = 2.696, CG = 0.001, CT = 21.984, 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 - 0.5743 + 0.5757 with an invariant (invariable) site category, proportion estimated - 0.3646 + 0.3650 Substitution rate categories under this model: rate proportion - 0.0000 0.3646 - 0.0479 0.1589 - 0.2977 0.1589 - 0.8676 0.1589 - 2.7869 0.1589 + 0.0000 0.3650 + 0.0481 0.1587 + 0.2985 0.1587 + 0.8684 0.1587 + 2.7850 0.1587 Model 2 Number of states = 2 (binary data) @@ -14893,7 +14791,7 @@ 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: 3.147 10.53 2.722 0.001 22.18 1 0.333 0.222 0.157 0.288 0.574 0.365 +rep 1: 3.121 10.44 2.696 0.001 21.98 1 0.333 0.222 0.157 0.288 0.576 0.365 Partition model subset 2: Model contains no estimated parameters @@ -15065,10 +14963,6 @@ Optimizing branchlengths... improved 0.060 lnL 1200 -3320.1462 0.010 1 1300 -3320.0857 0.010 1 -1400 -3320.0695 0.010 1 -1500 -3320.0226 0.010 1 -1600 -3320.0183 0.010 1 -1700 -3320.0152 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15169,82 +15063,76 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1774, seed 1373611375, best lnL -3319.819 +Search rep 1 (of 2) generation 1322, seed 210069055, best lnL -3320.070 gen current_lnL precision last_tree_imp -1774 -3319.8191 0.010 1 +1322 -3320.0695 0.010 1 +1400 -3320.0695 0.010 1 +1500 -3320.0226 0.010 1 +1600 -3320.0183 0.010 1 +1700 -3320.0152 0.010 1 1800 -3319.8191 0.010 1 1900 -3319.6008 0.010 1 2000 -3319.5579 0.010 1 2100 -3319.5506 0.010 1 2200 -3319.4670 0.010 1 -2300 -3319.3661 0.010 1 -2400 -3319.3307 0.010 1 -2500 -3319.3291 0.010 1 -2600 -3319.1278 0.010 1 -2700 -3319.1207 0.010 1 -2800 -3319.0998 0.010 1 -2900 -3319.0298 0.010 1 -3000 -3319.0197 0.010 1 -3100 -3319.0161 0.010 1 -3200 -3319.0102 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3318.9726 +Current score = -3319.3977 Performing final optimizations... -pass 1 : -3318.7957 (branch= 0.0051 alpha= 0.0261 pinv= 0.0122 eq freqs= 0.0001 rel rates= 0.0950 ins/del rates= 0.0383) -pass 2 : -3318.6763 (branch= 0.0297 alpha= 0.0000 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0770 ins/del rates= 0.0073) -pass 3 : -3318.5452 (branch= 0.0348 alpha= 0.0098 pinv= 0.0130 eq freqs= 0.0000 rel rates= 0.0615 ins/del rates= 0.0120) -pass 4 : -3318.4390 (branch= 0.0217 alpha= 0.0086 pinv= 0.0128 eq freqs= 0.0006 rel rates= 0.0541 ins/del rates= 0.0084) -pass 5 : -3318.3509 (branch= 0.0139 alpha= 0.0083 pinv= 0.0120 eq freqs= 0.0005 rel rates= 0.0481 ins/del rates= 0.0053) -pass 6 : -3318.2777 (branch= 0.0086 alpha= 0.0086 pinv= 0.0112 eq freqs= 0.0000 rel rates= 0.0412 ins/del rates= 0.0036) -pass 7 : -3318.2133 (branch= 0.0060 alpha= 0.0084 pinv= 0.0103 eq freqs= 0.0003 rel rates= 0.0369 ins/del rates= 0.0024) -pass 8 : -3318.1590 (branch= 0.0038 alpha= 0.0083 pinv= 0.0094 eq freqs= 0.0000 rel rates= 0.0312 ins/del rates= 0.0016) -pass 9 : -3318.1116 (branch= 0.0024 alpha= 0.0077 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0275 ins/del rates= 0.0010) -pass 10: -3318.0704 (branch= 0.0015 alpha= 0.0073 pinv= 0.0078 eq freqs= 0.0000 rel rates= 0.0238 ins/del rates= 0.0007) -pass 11: -3318.0344 (branch= 0.0010 alpha= 0.0068 pinv= 0.0071 eq freqs= 0.0000 rel rates= 0.0206 ins/del rates= 0.0004) -pass 12: -3318.0030 (branch= 0.0006 alpha= 0.0063 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0179 ins/del rates= 0.0003) -pass 13: -3317.9754 (branch= 0.0004 alpha= 0.0058 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0154 ins/del rates= 0.0002) -pass 14: -3317.9512 (branch= 0.0003 alpha= 0.0053 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0001) -pass 15: -3317.9301 (branch= 0.0002 alpha= 0.0048 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0115 ins/del rates= 0.0001) -pass 16: -3317.9115 (branch= 0.0001 alpha= 0.0043 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0100 ins/del rates= 0.0000) -pass 17: -3317.8953 (branch= 0.0001 alpha= 0.0039 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0086 ins/del rates= 0.0000) -pass 18: -3317.8812 (branch= 0.0000 alpha= 0.0034 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0074 ins/del rates= 0.0000) -pass 19: -3317.8687 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0065 ins/del rates= 0.0000) -pass 20: -3317.8579 (branch= 0.0000 alpha= 0.0027 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0056 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8036 (branch= 0.0000 alpha= 0.0141 pinv= 0.0130 eq freqs= 0.0001 rel rates= 0.0270 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7907 (branch= 0.0001 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0063 ins/del rates= 0.0000) +pass 1 : -3319.0931 (branch= 0.0080 alpha= 0.0101 pinv= 0.0166 eq freqs= 0.0072 rel rates= 0.1959 ins/del rates= 0.0667) +pass 2 : -3318.8984 (branch= 0.0314 alpha= 0.0122 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.1261 ins/del rates= 0.0090) +pass 3 : -3318.7315 (branch= 0.0285 alpha= 0.0135 pinv= 0.0147 eq freqs= 0.0035 rel rates= 0.0994 ins/del rates= 0.0075) +pass 4 : -3318.6018 (branch= 0.0143 alpha= 0.0112 pinv= 0.0142 eq freqs= 0.0000 rel rates= 0.0846 ins/del rates= 0.0053) +pass 5 : -3318.4887 (branch= 0.0121 alpha= 0.0109 pinv= 0.0134 eq freqs= 0.0015 rel rates= 0.0712 ins/del rates= 0.0040) +pass 6 : -3318.3940 (branch= 0.0071 alpha= 0.0107 pinv= 0.0125 eq freqs= 0.0006 rel rates= 0.0609 ins/del rates= 0.0030) +pass 7 : -3318.3156 (branch= 0.0044 alpha= 0.0099 pinv= 0.0116 eq freqs= 0.0001 rel rates= 0.0504 ins/del rates= 0.0019) +pass 8 : -3318.2471 (branch= 0.0031 alpha= 0.0098 pinv= 0.0107 eq freqs= 0.0001 rel rates= 0.0435 ins/del rates= 0.0013) +pass 9 : -3318.1880 (branch= 0.0020 alpha= 0.0090 pinv= 0.0098 eq freqs= 0.0001 rel rates= 0.0373 ins/del rates= 0.0009) +pass 10: -3318.1359 (branch= 0.0014 alpha= 0.0086 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0325 ins/del rates= 0.0006) +pass 11: -3318.0911 (branch= 0.0009 alpha= 0.0080 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0273 ins/del rates= 0.0004) +pass 12: -3318.0520 (branch= 0.0006 alpha= 0.0074 pinv= 0.0074 eq freqs= 0.0001 rel rates= 0.0233 ins/del rates= 0.0003) +pass 13: -3318.0180 (branch= 0.0004 alpha= 0.0068 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0199 ins/del rates= 0.0002) +pass 14: -3317.9883 (branch= 0.0003 alpha= 0.0062 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0001) +pass 15: -3317.9623 (branch= 0.0002 alpha= 0.0056 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0147 ins/del rates= 0.0001) +pass 16: -3317.9396 (branch= 0.0001 alpha= 0.0051 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0127 ins/del rates= 0.0000) +pass 17: -3317.9197 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0109 ins/del rates= 0.0000) +pass 18: -3317.9024 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0093 ins/del rates= 0.0000) +pass 19: -3317.8873 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) +pass 20: -3317.8740 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8075 (branch= 0.0000 alpha= 0.0172 pinv= 0.0158 eq freqs= 0.0001 rel rates= 0.0334 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7916 (branch= 0.0001 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0077 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7878 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0015 ins/del rates= 0.0000) +pass 50: -3317.7880 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0019 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) +pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 71: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 71: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 +Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.068, AG = 10.272, AT = 2.659, CG = 0.001, CT = 21.554, GT = 1.000 + AC = 3.066, AG = 10.268, AT = 2.657, 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 - 0.5749 + 0.5747 with an invariant (invariable) site category, proportion estimated - 0.3613 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3613 - 0.0480 0.1597 - 0.2981 0.1597 - 0.8680 0.1597 - 2.7860 0.1597 + 0.0000 0.3612 + 0.0479 0.1597 + 0.2979 0.1597 + 0.8678 0.1597 + 2.7864 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15270,13 +15158,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (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: 3.068 10.27 2.659 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15434,75 +15322,15 @@ 6400 -210.4468 0.010 1104 6600 -210.4214 0.010 1104 6800 -210.3964 0.010 1104 -7000 -210.3383 0.010 1104 -7200 -210.3217 0.010 1104 -7400 -210.2807 0.010 1104 -7600 -210.2625 0.010 1104 -7800 -210.1872 0.010 1104 -8000 -210.1732 0.010 1104 -8200 -210.1275 0.010 1104 -8400 -210.1090 0.010 1104 -8600 -210.0887 0.010 1104 -8800 -210.0539 0.010 1104 -9000 -210.0488 0.010 1104 -9200 -209.9764 0.010 1104 -9400 -209.9612 0.010 1104 -9600 -209.9440 0.010 1104 -9800 -209.9190 0.010 1104 -10000 -209.8863 0.010 1104 - Optimizing parameters... improved 0.506 lnL - Optimizing branchlengths... improved 0.011 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2377 0.3274 0.2094 0.2255 - Rate Heterogeneity Model: - 3 discrete gamma distributed rate categories, alpha param estimated - 4.1638 - with an invariant (invariable) site category, proportion estimated - 0.2915 - Substitution rate categories under this model: - rate proportion - 0.0000 0.2915 - 0.5194 0.2362 - 0.9260 0.2362 - 1.5546 0.2362 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - -Saving site likelihoods to file ch.n.G3.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 : -209.3693 - -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: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.164 0.291 - -Treelengths: - TL -rep 1: 2.284 - -Saving final tree from best search rep (#1) to ch.n.G3.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15573,31 +15401,52 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 991383469, best lnL -209.369 + generation 6810, seed 1788236282, best lnL -210.396 gen current_lnL precision last_tree_imp -10001 -209.3693 0.010 1104 +6810 -210.3964 0.010 1104 +6900 -210.3559 0.010 1104 +7000 -210.3383 0.010 1104 +7100 -210.3220 0.010 1104 +7200 -210.3217 0.010 1104 +7300 -210.2908 0.010 1104 +7400 -210.2807 0.010 1104 +7500 -210.2794 0.010 1104 +7600 -210.2625 0.010 1104 +7700 -210.2314 0.010 1104 +7800 -210.1872 0.010 1104 +7900 -210.1766 0.010 1104 +8000 -210.1732 0.010 1104 +8100 -210.1381 0.010 1104 +8200 -210.1275 0.010 1104 +8300 -210.1114 0.010 1104 +8400 -210.1090 0.010 1104 +8500 -210.1074 0.010 1104 +8600 -210.0887 0.010 1104 +Reached termination condition! +last topological improvement at gen 1104 +Improvement over last 500 gen = 0.04941 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 + AC = 3.918, AG = 6.885, AT = 0.186, CG = 6.926, CT = 11.159, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2377 0.3274 0.2094 0.2255 + (ACGT) 0.2363 0.3327 0.2105 0.2206 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 4.1638 + 1.8479 with an invariant (invariable) site category, proportion estimated - 0.2915 + 0.1920 Substitution rate categories under this model: rate proportion - 0.0000 0.2915 - 0.5194 0.2362 - 0.9260 0.2362 - 1.5546 0.2362 + 0.0000 0.1920 + 0.3352 0.2693 + 0.8372 0.2693 + 1.8275 0.2693 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -15605,15 +15454,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.3693 +Replicate 1 : -210.0887 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: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.164 0.291 +rep 1: 3.918 6.885 0.186 6.926 11.16 1 0.236 0.333 0.210 0.221 1.848 0.192 Treelengths: TL -rep 1: 2.284 +rep 1: 2.342 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log @@ -15760,79 +15609,15 @@ 5000 -165.6807 0.010 843 5200 -165.6629 0.010 843 5400 -165.5971 0.010 843 -5600 -165.4762 0.010 843 -5800 -165.3720 0.010 843 -6000 -165.3449 0.010 843 -6200 -165.2640 0.010 843 -6400 -165.1346 0.010 843 -6600 -165.0582 0.010 843 -6800 -165.0555 0.010 843 -7000 -164.9208 0.010 843 -7200 -164.7998 0.010 843 -7400 -164.7200 0.010 7384 -7600 -164.6617 0.010 7384 -7800 -164.5208 0.010 7384 -8000 -164.4381 0.010 7384 -8200 -164.2988 0.010 7384 -8400 -164.1759 0.010 7384 -8600 -164.1241 0.010 7384 -8800 -163.9560 0.010 7384 -9000 -163.8539 0.010 7384 -9200 -163.8476 0.010 7384 -9400 -163.7481 0.010 7384 -9600 -163.6368 0.010 7384 -9800 -163.5999 0.010 7384 -10000 -163.5758 0.010 7384 - Optimizing parameters... improved 1.517 lnL - Optimizing branchlengths... improved 0.024 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 0.623, AG = 8.557, AT = 1.923, CG = 3.484, CT = 32.948, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.1298 0.4236 0.2357 0.2109 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 525.3875 - with an invariant (invariable) site category, proportion estimated - 0.3606 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3606 - 0.9451 0.1599 - 0.9853 0.1599 - 1.0136 0.1599 - 1.0560 0.1599 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 3 branches were collapsed. - - -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 : -162.0348 - -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: 0.6227 8.557 1.923 3.484 32.95 1 0.130 0.424 0.236 0.211 525.388 0.361 - -Treelengths: - TL -rep 1: 3.169 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.n.G4.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -WARNING: Tree from prematurely terminated search saved to bootstrap file -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15904,11 +15689,60 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10001, seed 172398639, best lnL -162.035 +Bootstrap rep 1 (of 1) generation 5400, seed 16156446, best lnL -165.597 gen current_lnL precision last_tree_imp -10001 -162.0348 0.010 7384 +5400 -165.5971 0.010 843 +5500 -165.5242 0.010 843 +5600 -165.4762 0.010 843 +5700 -165.4315 0.010 843 +5800 -165.3720 0.010 843 +5900 -165.3458 0.010 843 +6000 -165.3449 0.010 843 +6100 -165.2859 0.010 843 +6200 -165.2640 0.010 843 +6300 -165.1568 0.010 843 +6400 -165.1346 0.010 843 +6500 -165.1038 0.010 843 +6600 -165.0582 0.010 843 +6700 -165.0566 0.010 843 +6800 -165.0555 0.010 843 +6900 -164.9353 0.010 843 +7000 -164.9208 0.010 843 +7100 -164.8347 0.010 843 +7200 -164.7998 0.010 843 +7300 -164.7626 0.010 843 +7400 -164.7200 0.010 7384 +7500 -164.6619 0.010 7384 +7600 -164.6617 0.010 7384 +7700 -164.5339 0.010 7384 +7800 -164.5208 0.010 7384 +7900 -164.4744 0.010 7384 +8000 -164.4381 0.010 7384 +8100 -164.3291 0.010 7384 +8200 -164.2988 0.010 7384 +8300 -164.1852 0.010 7384 +8400 -164.1759 0.010 7384 +8500 -164.1671 0.010 7384 +8600 -164.1241 0.010 7384 +8700 -163.9937 0.010 7384 +8800 -163.9560 0.010 7384 +8900 -163.9223 0.010 7384 +9000 -163.8539 0.010 7384 +9100 -163.8505 0.010 7384 +9200 -163.8476 0.010 7384 +9300 -163.7792 0.010 7384 +9400 -163.7481 0.010 7384 +9500 -163.7087 0.010 7384 +9600 -163.6368 0.010 7384 +9700 -163.6118 0.010 7384 +9800 -163.5999 0.010 7384 +9900 -163.5962 0.010 7384 +10000 -163.5758 0.010 7384 + Optimizing parameters... improved 1.517 lnL + Optimizing branchlengths... improved 0.024 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -15932,6 +15766,10 @@ 3 branches were collapsed. +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). @@ -15948,7 +15786,7 @@ Saving best tree to bootstrap file ch.n.G4.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -16097,52 +15935,15 @@ 9200 -212.5124 0.010 530 9400 -212.4972 0.010 530 9600 -212.4771 0.010 530 -9800 -212.4725 0.010 530 -10000 -212.4559 0.010 530 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 9.352, AG = 17.318, AT = 0.708, CG = 16.903, CT = 11.028, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2159 0.2906 0.1835 0.3100 - Rate Heterogeneity Model: - no rate heterogeneity - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. - -Saving site likelihoods to file ch.n.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 : -212.4558 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 9.352 17.32 0.7079 16.9 11.03 1 0.216 0.291 0.184 0.310 - -Treelengths: - TL -rep 1: 1.725 - -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 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -16213,15 +16014,19 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1932323236, best lnL -212.456 + generation 9730, seed 21424818, best lnL -212.474 gen current_lnL precision last_tree_imp -10001 -212.4558 0.010 530 +9730 -212.4742 0.010 530 +9800 -212.4725 0.010 530 +Reached termination condition! +last topological improvement at gen 530 +Improvement over last 500 gen = 0.03831 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 9.352, AG = 17.318, AT = 0.708, CG = 16.903, CT = 11.028, GT = 1.000 + AC = 8.646, AG = 16.278, AT = 0.684, CG = 16.326, CT = 10.419, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2159 0.2906 0.1835 0.3100 Rate Heterogeneity Model: @@ -16236,15 +16041,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.4558 +Replicate 1 : -212.4725 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 9.352 17.32 0.7079 16.9 11.03 1 0.216 0.291 0.184 0.310 +rep 1: 8.646 16.28 0.6836 16.33 10.42 1 0.216 0.291 0.184 0.310 Treelengths: TL -rep 1: 1.725 +rep 1: 1.722 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 @@ -16415,67 +16220,15 @@ 9200 -209.9408 0.010 8491 9400 -209.9288 0.010 8491 9600 -209.9140 0.010 8491 -9800 -209.9063 0.010 8491 -10000 -209.9022 0.010 8491 - Optimizing parameters... improved 0.499 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 2.427, AG = 4.433, AT = 0.045, CG = 4.623, CT = 8.877, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2434 0.3359 0.2135 0.2072 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 4.6841 - with an invariant (invariable) site category, proportion estimated - 0.3065 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3065 - 0.4884 0.1734 - 0.7960 0.1734 - 1.0838 0.1734 - 1.6318 0.1734 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. - - -NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with - a positive constraint, it is possible for a constrained branch itself to be collapsed. - If you care, be careful to check whether this has happened or turn off branch collapsing. - -Saving site likelihoods to file ch.n.const.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 : -209.4035 - -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: 2.427 4.433 0.04505 4.623 8.877 1 0.243 0.336 0.213 0.207 4.684 0.306 - -Treelengths: - TL -rep 1: 2.469 - -Saving final tree from best search rep (#1) to ch.n.const.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -16554,11 +16307,18 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1232396621, best lnL -209.403 + generation 9682, seed 1770947878, best lnL -209.914 gen current_lnL precision last_tree_imp -10001 -209.4035 0.010 8491 +9682 -209.9140 0.010 8491 +9700 -209.9140 0.010 8491 +9800 -209.9063 0.010 8491 +9900 -209.9029 0.010 8491 +10000 -209.9022 0.010 8491 + Optimizing parameters... improved 0.499 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -16587,6 +16347,11 @@ If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.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!*** + ####################################################### @@ -16605,6 +16370,8 @@ Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf @@ -16831,23 +16598,6 @@ Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 0.000 lnL 2100 -13370.4112 0.108 0 -2200 -13370.3996 0.108 0 -2300 -13370.3996 0.108 0 -2400 -13370.3948 0.108 0 -2500 -13370.3792 0.108 0 -Optimization precision reduced - Optimizing parameters... improved 0.001 lnL - Optimizing branchlengths... improved 0.000 lnL -2600 -13370.3703 0.010 0 -2700 -13370.3695 0.010 0 -2800 -13370.3692 0.010 0 -2900 -13370.3688 0.010 0 -3000 -13370.3644 0.010 0 -3100 -13370.3583 0.010 0 -3200 -13370.3526 0.010 0 -3300 -13370.3479 0.010 0 -3400 -13370.3478 0.010 0 -3500 -13370.3466 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16970,18 +16720,18 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3597, seed 323633943, best lnL -13370.346 +Bootstrap rep 1 (of 1) generation 2177, seed 1157214708, best lnL -13370.400 gen current_lnL precision last_tree_imp -3597 -13370.3463 0.010 0 +2177 -13370.3996 0.108 0 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.727, AG = 2.686, AT = 1.284, CG = 1.284, CT = 4.404, GT = 1.000 + AC = 1.663, AG = 2.639, AT = 1.246, CG = 1.246, CT = 4.221, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3076 0.1804 0.3103 0.2017 + (ACGT) 0.3082 0.1810 0.3087 0.2020 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3662 @@ -16989,45 +16739,45 @@ rate proportion 0.0122 0.2500 0.1561 0.2500 - 0.6920 0.2500 - 3.1397 0.2500 + 0.6919 0.2500 + 3.1398 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.623, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.623, GT = 1.000 + AC = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2819 0.1752 0.1596 0.3832 + (ACGT) 0.2814 0.1768 0.1593 0.3825 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2452 + 0.2449 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0632 0.2500 - 0.4912 0.2500 - 3.4437 0.2500 + 0.0630 0.2500 + 0.4906 0.2500 + 3.4445 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.630, CT = 5.303, GT = 1.000 + AC = 1.000, AG = 5.311, AT = 4.309, CG = 0.629, CT = 5.311, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3463 0.2762 0.2219 + (ACGT) 0.1554 0.3464 0.2763 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1990 + 4.1264 with an invariant (invariable) site category, proportion estimated - 0.0493 + 0.0487 Substitution rate categories under this model: rate proportion - 0.0000 0.0493 - 0.4650 0.2377 - 0.7818 0.2377 - 1.0843 0.2377 - 1.6689 0.2377 + 0.0000 0.0487 + 0.4612 0.2378 + 0.7795 0.2378 + 1.0844 0.2378 + 1.6750 0.2378 Subset rate multipliers: 0.53 0.29 2.18 @@ -17039,25 +16789,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3463 +Replicate 1 : -13370.3996 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: 1.727 2.686 1.284 1.284 4.404 1 0.308 0.180 0.310 0.202 0.366 +rep 1: 1.663 2.639 1.246 1.246 4.221 1 0.308 0.181 0.309 0.202 0.366 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: 2.623 4.225 0.813 4.225 2.623 1 0.282 0.175 0.160 0.383 0.245 +rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.245 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 5.303 4.268 0.6297 5.303 1 0.155 0.346 0.276 0.222 4.199 0.049 +rep 1: 1 5.311 4.309 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.767 0.531 0.287 2.183 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17279,7 +17029,7 @@ pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17365,6 +17115,34 @@ 800 -467.7328 0.010 0 900 -467.7315 0.010 0 1000 -467.7286 0.010 0 +1100 -467.7271 0.010 0 +1200 -467.7201 0.010 0 +1300 -467.7189 0.010 0 +1400 -467.7173 0.010 0 +1500 -467.7148 0.010 0 +1600 -467.7147 0.010 0 +1700 -467.7131 0.010 0 +1800 -467.7123 0.010 0 +1900 -467.7122 0.010 0 +2000 -467.7119 0.010 0 +2100 -467.7104 0.010 0 +2200 -467.7088 0.010 0 +2300 -467.7087 0.010 0 +2400 -467.7083 0.010 0 +2500 -467.7076 0.010 0 +2600 -467.7072 0.010 0 +2700 -467.7072 0.010 0 +2800 -467.7067 0.010 0 +2900 -467.7065 0.010 0 +3000 -467.7064 0.010 0 +3100 -467.7058 0.010 0 +3200 -467.7050 0.010 0 +3300 -467.7035 0.010 0 +3400 -467.7029 0.010 0 +3500 -467.7024 0.010 0 +3600 -467.7020 0.010 0 +3700 -467.7017 0.010 0 +3800 -467.7017 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17490,36 +17268,8 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1030, seed 1012448696, best lnL -467.728 +Search rep 2 (of 5) generation 3800, seed 218463189, best lnL -467.702 gen current_lnL precision last_tree_imp -1030 -467.7281 0.010 0 -1100 -467.7271 0.010 0 -1200 -467.7201 0.010 0 -1300 -467.7189 0.010 0 -1400 -467.7173 0.010 0 -1500 -467.7148 0.010 0 -1600 -467.7147 0.010 0 -1700 -467.7131 0.010 0 -1800 -467.7123 0.010 0 -1900 -467.7122 0.010 0 -2000 -467.7119 0.010 0 -2100 -467.7104 0.010 0 -2200 -467.7088 0.010 0 -2300 -467.7087 0.010 0 -2400 -467.7083 0.010 0 -2500 -467.7076 0.010 0 -2600 -467.7072 0.010 0 -2700 -467.7072 0.010 0 -2800 -467.7067 0.010 0 -2900 -467.7065 0.010 0 -3000 -467.7064 0.010 0 -3100 -467.7058 0.010 0 -3200 -467.7050 0.010 0 -3300 -467.7035 0.010 0 -3400 -467.7029 0.010 0 -3500 -467.7024 0.010 0 -3600 -467.7020 0.010 0 -3700 -467.7017 0.010 0 3800 -467.7017 0.010 0 3900 -467.7013 0.010 0 4000 -467.7004 0.010 0 @@ -17549,7 +17299,7 @@ pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17657,26 +17407,39 @@ 3000 -467.7153 0.010 0 3100 -467.7148 0.010 0 3200 -467.7140 0.010 0 +3300 -467.7139 0.010 0 +3400 -467.7136 0.010 0 +3500 -467.7136 0.010 0 +3600 -467.7132 0.010 0 +3700 -467.7130 0.010 0 +3800 -467.7129 0.010 0 +3900 -467.7124 0.010 0 +4000 -467.7117 0.010 0 +4100 -467.7113 0.010 0 +4200 -467.7110 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7140 +Current score = -467.7107 Performing final optimizations... -pass 1 : -467.7140 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.7016 (branch= 0.0125 subset rates= 0.0000) -pass 3 : -467.6934 (branch= 0.0082 subset rates= 0.0000) -pass 4 : -467.6890 (branch= 0.0044 subset rates= 0.0000) -pass 5 : -467.6857 (branch= 0.0034 subset rates= 0.0000) -pass 6 : -467.6827 (branch= 0.0029 subset rates= 0.0001) -pass 7 : -467.6811 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -467.6800 (branch= 0.0012 subset rates= 0.0000) -pass 9 : -467.6796 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6787 (branch= 0.0003 subset rates= 0.0006) -pass 11: -467.6785 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6784 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7107 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7015 (branch= 0.0092 subset rates= 0.0000) +pass 3 : -467.6890 (branch= 0.0125 subset rates= 0.0000) +pass 4 : -467.6863 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -467.6849 (branch= 0.0014 subset rates= 0.0000) +pass 6 : -467.6820 (branch= 0.0029 subset rates= 0.0000) +pass 7 : -467.6809 (branch= 0.0012 subset rates= 0.0000) +pass 8 : -467.6799 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -467.6794 (branch= 0.0005 subset rates= 0.0000) +pass 10: -467.6792 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6791 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6790 (branch= 0.0001 subset rates= 0.0000) +pass 13: -467.6787 (branch= 0.0000 subset rates= 0.0003) +pass 14: -467.6785 (branch= 0.0002 subset rates= 0.0000) +pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 16: -467.6782 (branch= 0.0000 subset rates= 0.0002) +pass 17: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 18: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6783 +Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17723,8 +17486,8 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6797 -Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6783 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -467.6782 (same topology as 1) +Replicate 3 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17741,9 +17504,9 @@ TL R(1) R(2) R(3) rep 1: 3.838 0.789 1.477 2.150 rep 2: 3.842 0.786 1.478 2.181 -rep 3: 3.845 0.785 1.482 2.187 +rep 3: 3.844 0.786 1.479 2.188 -Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -17957,7 +17720,7 @@ pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18050,19 +17813,6 @@ 1200 -477.2713 0.010 510 1300 -477.2708 0.010 510 1400 -477.2690 0.010 510 -1500 -477.2686 0.010 510 -1600 -477.2682 0.010 510 -1700 -477.2659 0.010 510 -1800 -477.2652 0.010 510 -1900 -477.2634 0.010 510 -2000 -477.2631 0.010 510 -2100 -477.2605 0.010 510 -2200 -477.2601 0.010 510 -2300 -477.2592 0.010 510 -2400 -477.2590 0.010 510 -2500 -477.2586 0.010 510 -2600 -477.2586 0.010 510 -2700 -477.2584 0.010 510 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18188,9 +17938,22 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2721, seed 178883962, best lnL -477.258 +Search rep 2 (of 5) generation 1483, seed 2003160843, best lnL -477.269 gen current_lnL precision last_tree_imp -2721 -477.2584 0.010 510 +1483 -477.2686 0.010 510 +1500 -477.2686 0.010 510 +1600 -477.2682 0.010 510 +1700 -477.2659 0.010 510 +1800 -477.2652 0.010 510 +1900 -477.2634 0.010 510 +2000 -477.2631 0.010 510 +2100 -477.2605 0.010 510 +2200 -477.2601 0.010 510 +2300 -477.2592 0.010 510 +2400 -477.2590 0.010 510 +2500 -477.2586 0.010 510 +2600 -477.2586 0.010 510 +2700 -477.2584 0.010 510 2800 -477.2581 0.010 510 2900 -477.2571 0.010 510 3000 -477.2519 0.010 510 @@ -18461,32 +18224,29 @@ 0 -477.8447 0.010 0 100 -477.7601 0.010 42 200 -477.7377 0.010 42 -300 -477.7206 0.010 42 -400 -477.5657 0.010 324 -500 -477.5326 0.010 417 -600 -477.5291 0.010 417 -700 -477.5243 0.010 417 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.5198 +Current score = -477.7290 Performing final optimizations... -pass 1 : -477.4985 (branch= 0.0213 subset rates= 0.0000) -pass 2 : -477.4868 (branch= 0.0116 subset rates= 0.0001) -pass 3 : -477.4577 (branch= 0.0291 subset rates= 0.0000) -pass 4 : -477.4478 (branch= 0.0099 subset rates= 0.0000) -pass 5 : -477.4405 (branch= 0.0073 subset rates= 0.0000) -pass 6 : -477.4364 (branch= 0.0039 subset rates= 0.0002) -pass 7 : -477.4343 (branch= 0.0021 subset rates= 0.0000) -pass 8 : -477.4330 (branch= 0.0013 subset rates= 0.0000) -pass 9 : -477.4324 (branch= 0.0006 subset rates= 0.0000) -pass 10: -477.4321 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4318 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.7146 (branch= 0.0139 subset rates= 0.0005) +pass 2 : -477.6905 (branch= 0.0242 subset rates= 0.0000) +pass 3 : -477.6557 (branch= 0.0337 subset rates= 0.0010) +pass 4 : -477.6371 (branch= 0.0186 subset rates= 0.0000) +pass 5 : -477.6281 (branch= 0.0090 subset rates= 0.0000) +pass 6 : -477.6227 (branch= 0.0053 subset rates= 0.0001) +pass 7 : -477.6212 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -477.6201 (branch= 0.0011 subset rates= 0.0000) +pass 9 : -477.6186 (branch= 0.0004 subset rates= 0.0011) +pass 10: -477.6179 (branch= 0.0006 subset rates= 0.0000) +pass 11: -477.6177 (branch= 0.0003 subset rates= 0.0000) +pass 12: -477.6171 (branch= 0.0001 subset rates= 0.0004) +pass 13: -477.6169 (branch= 0.0002 subset rates= 0.0000) +pass 14: -477.6169 (branch= 0.0001 subset rates= 0.0000) +pass 15: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 17: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 18: -477.6168 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4318 +Final score = -477.6168 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18515,9 +18275,9 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.92 2.73 + 0.63 1.91 2.73 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. >>>Terminated Search rep 4 (of 5)<<< @@ -18535,7 +18295,7 @@ Replicate 1 : -477.2119 (best) Replicate 2 : -477.2121 (same topology as 1) Replicate 3 : -477.4316 -Replicate 4 : -477.4318 (same topology as 3) (TERMINATED PREMATURELY) +Replicate 4 : -477.6168 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18553,7 +18313,7 @@ rep 1: 4.671 0.643 1.908 2.618 rep 2: 4.668 0.644 1.904 2.619 rep 3: 4.930 0.631 1.914 2.747 -rep 4: 4.925 0.633 1.916 2.725 +rep 4: 4.890 0.634 1.909 2.730 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18851,6 +18611,13 @@ 1300 -425.6381 0.010 722 1400 -425.6345 0.010 722 1500 -425.6341 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6239 0.010 722 +1800 -425.6235 0.010 722 +1900 -425.6225 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6196 0.010 722 +2200 -425.6174 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18979,15 +18746,8 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1583, seed 1109948398, best lnL -425.628 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 2200, seed 1568714904, best lnL -425.617 gen current_lnL precision last_tree_imp -1583 -425.6282 0.010 722 -1600 -425.6274 0.010 722 -1700 -425.6239 0.010 722 -1800 -425.6235 0.010 722 -1900 -425.6225 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6196 0.010 722 2200 -425.6174 0.010 722 2300 -425.6146 0.010 722 2400 -425.6135 0.010 722 @@ -19023,7 +18783,7 @@ pass 13: -425.5492 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5492 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19108,23 +18868,120 @@ 3500 -425.3566 0.010 803 3600 -425.3560 0.010 803 3700 -425.3555 0.010 803 +3800 -425.3551 0.010 803 +3900 -425.3542 0.010 803 +4000 -425.3542 0.010 803 +4100 -425.3538 0.010 803 +4200 -425.3536 0.010 803 +4300 -425.3535 0.010 803 +4400 -425.3534 0.010 803 +Reached termination condition! +last topological improvement at gen 803 +Improvement over last 500 gen = 0.00083 +Current score = -425.3534 +Performing final optimizations... +pass 1 : -425.3485 (branch= 0.0000 subset rates= 0.0049) +pass 2 : -425.3321 (branch= 0.0164 subset rates= 0.0000) +pass 3 : -425.3250 (branch= 0.0071 subset rates= 0.0000) +pass 4 : -425.3223 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -425.3220 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -425.3220 (branch= 0.0000 subset rates= 0.0000) +pass 7 : -425.3215 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -425.3208 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -425.3207 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3206 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3205 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.3205 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.86 1.55 1.15 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1573911897 + +Initial ln Likelihood: -585.3657 +optimizing: starting branch lengths, subset rates... +pass 1:+ 128.924 (branch= 128.21 scale= 0.69 subset rates= 0.02) +pass 2:+ 11.959 (branch= 11.78 scale= 0.03 subset rates= 0.15) +pass 3:+ 4.421 (branch= 4.33 scale= 0.00 subset rates= 0.09) +pass 4:+ 0.779 (branch= 0.76 scale= 0.00 subset rates= 0.01) +pass 5:+ 0.057 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2135 +gen current_lnL precision last_tree_imp +0 -439.2135 0.010 0 +100 -428.1779 0.010 67 +200 -427.4638 0.010 189 +300 -427.4437 0.010 226 +400 -427.1435 0.010 393 +500 -427.1285 0.010 393 +600 -427.1120 0.010 393 +700 -427.1022 0.010 393 +800 -427.1003 0.010 393 +900 -427.0977 0.010 393 +1000 -427.0972 0.010 393 +1100 -427.0948 0.010 393 +1200 -427.0919 0.010 393 +1300 -427.0909 0.010 393 +1400 -427.0892 0.010 393 +1500 -427.0880 0.010 393 +1600 -427.0868 0.010 393 +1700 -427.0861 0.010 393 +1800 -427.0846 0.010 393 +1900 -425.5433 0.010 1890 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.3555 +Current score = -425.5083 Performing final optimizations... -pass 1 : -425.3500 (branch= 0.0000 subset rates= 0.0055) -pass 2 : -425.3331 (branch= 0.0169 subset rates= 0.0000) -pass 3 : -425.3244 (branch= 0.0087 subset rates= 0.0000) -pass 4 : -425.3225 (branch= 0.0019 subset rates= 0.0000) -pass 5 : -425.3225 (branch= 0.0000 subset rates= 0.0000) -pass 6 : -425.3223 (branch= 0.0002 subset rates= 0.0000) -pass 7 : -425.3210 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -425.3202 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -425.3201 (branch= 0.0000 subset rates= 0.0000) -pass 10: -425.3201 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.3201 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3200 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3809 (branch= 0.1253 subset rates= 0.0021) +pass 2 : -425.3357 (branch= 0.0451 subset rates= 0.0001) +pass 3 : -425.3290 (branch= 0.0067 subset rates= 0.0000) +pass 4 : -425.3262 (branch= 0.0029 subset rates= 0.0000) +pass 5 : -425.3230 (branch= 0.0031 subset rates= 0.0000) +pass 6 : -425.3218 (branch= 0.0012 subset rates= 0.0000) +pass 7 : -425.3212 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -425.3207 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -425.3204 (branch= 0.0002 subset rates= 0.0000) +pass 10: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.3200 +Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -19155,9 +19012,9 @@ Subset rate multipliers: 0.86 1.54 1.15 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 3 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -19165,14 +19022,15 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 Replicate 2 : -425.5492 -Replicate 3 : -425.3200 (best) (TERMINATED PREMATURELY) +Replicate 3 : -425.3205 +Replicate 4 : -425.3204 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19189,9 +19047,10 @@ TL R(1) R(2) R(3) rep 1: 3.038 0.868 1.530 1.121 rep 2: 3.039 0.868 1.535 1.108 -rep 3: 2.979 0.865 1.538 1.146 +rep 3: 2.976 0.862 1.548 1.149 +rep 4: 2.980 0.865 1.538 1.145 -Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#4) to bootstrap file ch.p.mkv.ssr.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### @@ -19499,15 +19358,6 @@ 500 -474.5695 0.010 496 600 -474.0703 0.010 585 700 -474.0481 0.010 585 -800 -474.0412 0.010 585 -900 -474.0316 0.010 585 -1000 -474.0282 0.010 585 -1100 -474.0225 0.010 585 -1200 -474.0142 0.010 585 -1300 -474.0116 0.010 585 -1400 -474.0080 0.010 585 -1500 -474.0041 0.010 585 -1600 -474.0016 0.010 585 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19633,9 +19483,18 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1641, seed 894358758, best lnL -474.002 +Search rep 2 (of 5) generation 729, seed 1447960421, best lnL -474.043 gen current_lnL precision last_tree_imp -1641 -474.0016 0.010 585 +729 -474.0429 0.010 585 +800 -474.0412 0.010 585 +900 -474.0316 0.010 585 +1000 -474.0282 0.010 585 +1100 -474.0225 0.010 585 +1200 -474.0142 0.010 585 +1300 -474.0116 0.010 585 +1400 -474.0080 0.010 585 +1500 -474.0041 0.010 585 +1600 -474.0016 0.010 585 1700 -474.0010 0.010 585 1800 -473.9994 0.010 585 1900 -473.9983 0.010 585 @@ -19672,7 +19531,7 @@ pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19787,144 +19646,31 @@ 3600 -474.4611 0.010 535 3700 -474.4608 0.010 535 3800 -474.4608 0.010 535 -3900 -474.4607 0.010 535 -4000 -474.4607 0.010 535 -Reached termination condition! -last topological improvement at gen 535 -Improvement over last 500 gen = 0.00071 -Current score = -474.4607 -Performing final optimizations... -pass 1 : -474.4602 (branch= 0.0000 subset rates= 0.0005) -pass 2 : -474.4430 (branch= 0.0172 subset rates= 0.0000) -pass 3 : -474.4430 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -474.4383 (branch= 0.0047 subset rates= 0.0000) -pass 5 : -474.4338 (branch= 0.0046 subset rates= 0.0000) -pass 6 : -474.4316 (branch= 0.0021 subset rates= 0.0000) -pass 7 : -474.4301 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -474.4294 (branch= 0.0006 subset rates= 0.0001) -pass 9 : -474.4289 (branch= 0.0005 subset rates= 0.0000) -pass 10: -474.4285 (branch= 0.0003 subset rates= 0.0000) -pass 11: -474.4283 (branch= 0.0002 subset rates= 0.0001) -pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.4281 (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) -Looking for minimum length branches... -Final score = -474.4281 -Time used so far = 0 hours, 0 minutes and 10 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.03 2.92 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< - ->>>Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=17311967 - -Initial ln Likelihood: -692.6191 -optimizing: starting branch lengths, subset rates... -pass 1:+ 190.070 (branch= 177.15 scale= 2.85 subset rates= 10.07) -pass 2:+ 19.411 (branch= 14.64 scale= 0.00 subset rates= 4.77) -pass 3:+ 6.755 (branch= 5.00 scale= 0.00 subset rates= 1.76) -pass 4:+ 1.362 (branch= 0.80 scale= 0.00 subset rates= 0.57) -pass 5:+ 0.119 (branch= 0.09 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.014 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8346 -gen current_lnL precision last_tree_imp -0 -474.8346 0.010 0 -100 -474.7468 0.010 62 -200 -474.1733 0.010 145 -300 -474.1512 0.010 145 -400 -474.1334 0.010 145 -500 -474.0520 0.010 463 -600 -474.0182 0.010 523 -700 -474.0118 0.010 523 -800 -474.0048 0.010 523 -900 -474.0037 0.010 523 -1000 -473.9971 0.010 523 -1100 -473.9952 0.010 523 -1200 -473.9905 0.010 523 -1300 -473.9889 0.010 523 -1400 -473.9874 0.010 523 -1500 -473.9858 0.010 523 -1600 -473.9833 0.010 523 -1700 -473.9805 0.010 523 -1800 -473.9803 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9795 +Current score = -474.4607 Performing final optimizations... -pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0026) -pass 2 : -473.9606 (branch= 0.0156 subset rates= 0.0008) -pass 3 : -473.9568 (branch= 0.0039 subset rates= 0.0000) -pass 4 : -473.9558 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9549 (branch= 0.0010 subset rates= 0.0000) -pass 6 : -473.9530 (branch= 0.0012 subset rates= 0.0007) -pass 7 : -473.9516 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4607 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -474.4435 (branch= 0.0172 subset rates= 0.0000) +pass 3 : -474.4435 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -474.4393 (branch= 0.0042 subset rates= 0.0000) +pass 5 : -474.4350 (branch= 0.0043 subset rates= 0.0000) +pass 6 : -474.4331 (branch= 0.0020 subset rates= 0.0000) +pass 7 : -474.4317 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -474.4297 (branch= 0.0006 subset rates= 0.0013) +pass 9 : -474.4293 (branch= 0.0005 subset rates= 0.0000) +pass 10: -474.4289 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.4288 (branch= 0.0002 subset rates= 0.0000) +pass 12: -474.4287 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4287 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4284 (branch= 0.0000 subset rates= 0.0003) +pass 15: -474.4283 (branch= 0.0000 subset rates= 0.0000) +pass 16: -474.4283 (branch= 0.0000 subset rates= 0.0000) +pass 17: -474.4282 (branch= 0.0000 subset rates= 0.0001) +pass 18: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 19: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 20: -474.4282 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9508 +Final score = -474.4282 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -19953,11 +19699,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -19965,15 +19711,14 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9508 -Replicate 2 : -473.9508 (same topology as 1) -Replicate 3 : -474.4281 -Replicate 4 : -473.9508 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -473.9508 (best) (same topology as 1) +Replicate 3 : -474.4282 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19990,10 +19735,9 @@ TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.066 2.813 rep 2: 4.349 0.588 2.064 2.806 -rep 3: 4.601 0.587 2.035 2.918 -rep 4: 4.351 0.587 2.066 2.810 +rep 3: 4.600 0.588 2.031 2.921 -Saving final tree from best search rep (#4) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -20009,7 +19753,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j12 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j16 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' @@ -20058,11 +19802,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. -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_amd64.deb'. +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -20070,12 +19814,14 @@ 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/1370477/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1370477/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/3262707 and its subdirectories -I: Current time: Mon Aug 25 23:27:55 -12 2025 -I: pbuilder-time-stamp: 1756207675 +I: removing directory /srv/workspace/pbuilder/1370477 and its subdirectories +I: Current time: Tue Sep 29 07:56:56 +14 2026 +I: pbuilder-time-stamp: 1790618216