Diff of the two buildlogs: -- --- b1/build.log 2024-12-21 13:22:05.255169571 +0000 +++ b2/build.log 2024-12-21 13:36:20.420112462 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 21 01:07:05 -12 2024 -I: pbuilder-time-stamp: 1734786425 +I: Current time: Sun Dec 22 03:22:34 +14 2024 +I: pbuilder-time-stamp: 1734787354 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/1706/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20841/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 21 13:22 /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/20841/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20841/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='85f3f2394b694b0eb4789112db88fd11' - 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='1706' - PS1='# ' - PS2='> ' + INVOCATION_ID=12f63c5a254946f6b3735a18a786798d + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=20841 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.KeF3B9Kp/pbuilderrc_kBOc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KeF3B9Kp/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.KeF3B9Kp/pbuilderrc_E3Bq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KeF3B9Kp/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1706/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/20841/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -166,7 +198,7 @@ Get: 49 http://deb.debian.org/debian unstable/main armhf libncl-dev armhf 2.1.21+git20210811.b1213a7-6 [537 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf mpi-default-dev armhf 1.17 [3148 B] Get: 51 http://deb.debian.org/debian unstable/main armhf ncl-tools armhf 2.1.21+git20210811.b1213a7-6 [130 kB] -Fetched 35.8 MB in 1s (50.9 MB/s) +Fetched 35.8 MB in 1s (26.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19681 files and directories currently installed.) @@ -392,7 +424,11 @@ 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/20841/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/20841/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 @@ -494,8 +530,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -564,7 +600,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -573,6 +609,29 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -617,6 +676,23 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -673,7 +749,31 @@ 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 configoptions.cpp:20: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': -configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 337 | sprintf(modName, "model%d", modelNum); - | ^~ -configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp + 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) + | ^~~~~~~ +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{ | ^~~~~~~~~~~~~~~ @@ -830,7 +940,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -875,8 +985,7 @@ 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{ | ^~~~~~~~~~~~~~~ @@ -924,26 +1033,13 @@ /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: + 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 | ^~~~~~~~~~~~~~~ @@ -1049,28 +1157,10 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from 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/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 | ^~~~~~~~~~~~~~~ @@ -1168,10 +1282,6 @@ /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 >; _ForwardIterator = ProcessedNxsToken*]': @@ -1179,68 +1289,14 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:316:21: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:713:33, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:2004:32, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:1321:19, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:1933:18, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:882:26, - inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:137:7, - inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:320:17: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp In file included from tree.h:35, - from individual.h:21, - from model.cpp:26: + from optimization.cpp:19: 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 model.cpp:17: +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 | ^~~~~~~~~~~~~~~ @@ -1271,6 +1327,15 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1624:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:238:44, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:316:21: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -1278,6 +1343,31 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:713:33, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:2004:32, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:1321:19, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:1933:18, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_list.h:882:26, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:137:7, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/list.tcc:320:17: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from 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 Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': +optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ + | ^ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1314,60 +1404,6 @@ 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, - from optimization.cpp:19: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 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 Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': -optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ - | ^ -In file included from tree.h:35, from individual.h:21, from population.h:31, from population.cpp:45: @@ -1423,6 +1459,30 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: @@ -1463,29 +1523,7 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1503,6 +1541,8 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); @@ -1519,8 +1559,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1540,11 +1578,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1601,58 +1635,6 @@ tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from mpitrick.cpp:27: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from mpitrick.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_function.h:1435: -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1720,21 +1702,16 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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{ @@ -1960,6 +2019,22 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2012,15 +2087,39 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i >; _ForwardIterator = ProcessedNxsToken*]': -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': +linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1322 | register int nsq = n * n; + | ^~~ 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, @@ -2506,6 +2525,30 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/ncl/ncl.h:27, + from garlireader.cpp:41: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +In file included from /usr/include/c++/14/vector:65, + from /usr/include/ncl/ncl.h:60: +/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, @@ -2531,13 +2574,6 @@ /usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -2589,41 +2625,6 @@ 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2678,6 +2679,42 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2734,6 +2771,30 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: @@ -2779,13 +2840,7 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2797,12 +2852,16 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from population.cpp:25: + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2830,32 +2889,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2912,28 +2946,7 @@ tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from treenode.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -3001,6 +3014,29 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from treenode.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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, @@ -3036,7 +3072,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -6003,7 +6039,7 @@ 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 46 seconds +Time used = 0 hours, 0 minutes and 45 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6155,7 +6191,7 @@ 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 32 seconds +Time used = 0 hours, 0 minutes and 31 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6729,7 +6765,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6884,7 +6920,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7051,7 +7087,7 @@ pass 15: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9539,7 +9575,7 @@ 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 10 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -12829,7 +12865,6 @@ 100 -93.0240 0.500 0 200 -91.3705 0.500 199 300 -90.7565 0.500 215 -400 -90.4959 0.500 215 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12926,9 +12961,10 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 406, seed 372905919, best lnL -90.496 +Bootstrap rep 1 (of 1) generation 397, seed 1523457500, best lnL -90.496 gen current_lnL precision last_tree_imp -406 -90.4959 0.500 215 +397 -90.4959 0.500 215 +400 -90.4959 0.500 215 500 -90.3850 0.500 215 600 -90.2906 0.500 215 700 -90.2169 0.500 215 @@ -13106,6 +13142,7 @@ 0 -116.1434 0.500 0 100 -112.9555 0.500 84 200 -112.4964 0.500 84 +300 -112.3224 0.500 84 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13192,10 +13229,9 @@ STARTING RUN Restarting from checkpoint... - generation 293, seed 1787713630, best lnL -112.347 + generation 309, seed 980534317, best lnL -112.316 gen current_lnL precision last_tree_imp -293 -112.3466 0.500 84 -300 -112.3224 0.500 84 +309 -112.3158 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 600 -111.7788 0.500 84 @@ -13383,6 +13419,7 @@ Optimization precision reduced Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL +1200 -111.6824 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13468,9 +13505,9 @@ STARTING RUN Restarting from checkpoint... - generation 1190, seed 502148953, best lnL -111.682 + generation 1223, seed 1312840177, best lnL -111.682 gen current_lnL precision last_tree_imp -1190 -111.6824 0.010 563 +1223 -111.6823 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13494,7 +13531,7 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6824 +Replicate 1 : -111.6823 Parameter estimates: Model contains no estimated parameters @@ -13715,9 +13752,9 @@ STARTING RUN Restarting from checkpoint... - generation 14, seed 1752200983, best lnL -206.464 + generation 16, seed 1304835690, best lnL -206.434 gen current_lnL precision last_tree_imp -14 -206.4639 0.500 13 +16 -206.4341 0.500 13 20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 @@ -13911,6 +13948,7 @@ lnL after optimization: -195.4001 gen current_lnL precision last_tree_imp 0 -195.4001 0.500 0 +10 -195.3555 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13998,9 +14036,8 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 9, seed 1495170053, best lnL -195.355 +Bootstrap rep 1 (of 1) generation 10, seed 1509658266, best lnL -195.355 gen current_lnL precision last_tree_imp -9 -195.3555 0.500 0 10 -195.3555 0.500 0 20 -195.3342 0.500 0 30 -195.2777 0.500 0 @@ -14223,7 +14260,6 @@ Optimization precision reduced Optimizing parameters... improved 0.833 lnL Optimizing branchlengths... improved 0.085 lnL -1100 -3352.7168 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14327,9 +14363,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1156, seed 2088773856, best lnL -3352.656 +Search rep 1 (of 2) generation 1085, seed 1049534661, best lnL -3352.720 gen current_lnL precision last_tree_imp -1156 -3352.6556 0.010 0 +1085 -3352.7196 0.010 0 +1100 -3352.7168 0.010 0 1200 -3352.6373 0.010 0 1300 -3352.5144 0.010 0 1400 -3352.4046 0.010 0 @@ -14338,65 +14375,64 @@ 1700 -3352.2857 0.010 0 1800 -3352.2040 0.010 0 1900 -3351.8438 0.010 0 -2000 -3351.7704 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.7704 +Current score = -3351.7779 Performing final optimizations... -pass 1 : -3351.6174 (branch= 0.0000 alpha= 0.0241 pinv= 0.0191 eq freqs= 0.0001 rel rates= 0.1044 subset rates= 0.0053) -pass 2 : -3351.4153 (branch= 0.0163 alpha= 0.0089 pinv= 0.0179 eq freqs= 0.0264 rel rates= 0.1312 subset rates= 0.0013) -pass 3 : -3351.2448 (branch= 0.0165 alpha= 0.0136 pinv= 0.0165 eq freqs= 0.0023 rel rates= 0.1166 subset rates= 0.0049) -pass 4 : -3351.1081 (branch= 0.0105 alpha= 0.0120 pinv= 0.0155 eq freqs= 0.0010 rel rates= 0.0952 subset rates= 0.0025) -pass 5 : -3350.9885 (branch= 0.0093 alpha= 0.0117 pinv= 0.0146 eq freqs= 0.0009 rel rates= 0.0805 subset rates= 0.0026) -pass 6 : -3350.8882 (branch= 0.0053 alpha= 0.0113 pinv= 0.0136 eq freqs= 0.0002 rel rates= 0.0678 subset rates= 0.0022) -pass 7 : -3350.8006 (branch= 0.0040 alpha= 0.0107 pinv= 0.0125 eq freqs= 0.0002 rel rates= 0.0590 subset rates= 0.0012) -pass 8 : -3350.7260 (branch= 0.0030 alpha= 0.0108 pinv= 0.0115 eq freqs= 0.0002 rel rates= 0.0491 subset rates= 0.0000) -pass 9 : -3350.6589 (branch= 0.0005 alpha= 0.0103 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0443 subset rates= 0.0014) -pass 10: -3350.6016 (branch= 0.0016 alpha= 0.0097 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0357 subset rates= 0.0000) -pass 11: -3350.5531 (branch= 0.0004 alpha= 0.0085 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0309 subset rates= 0.0000) -pass 12: -3350.5094 (branch= 0.0001 alpha= 0.0085 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0263 subset rates= 0.0011) -pass 13: -3350.4732 (branch= 0.0006 alpha= 0.0073 pinv= 0.0070 eq freqs= 0.0001 rel rates= 0.0212 subset rates= 0.0000) -pass 14: -3350.4417 (branch= 0.0001 alpha= 0.0065 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0186 subset rates= 0.0000) -pass 15: -3350.4140 (branch= 0.0000 alpha= 0.0061 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0160 subset rates= 0.0000) -pass 16: -3350.3897 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0137 subset rates= 0.0000) -pass 17: -3350.3687 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0117 subset rates= 0.0000) -pass 18: -3350.3504 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) -pass 19: -3350.3346 (branch= 0.0000 alpha= 0.0039 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0085 subset rates= 0.0000) -pass 20: -3350.3209 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0073 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2532 (branch= 0.0000 alpha= 0.0172 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0347 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2378 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0081 subset rates= 0.0000) +pass 1 : -3351.5926 (branch= 0.0000 alpha= 0.0226 pinv= 0.0190 eq freqs= 0.0001 rel rates= 0.1388 subset rates= 0.0049) +pass 2 : -3351.4028 (branch= 0.0113 alpha= 0.0087 pinv= 0.0182 eq freqs= 0.0253 rel rates= 0.1262 subset rates= 0.0000) +pass 3 : -3351.2338 (branch= 0.0180 alpha= 0.0145 pinv= 0.0163 eq freqs= 0.0018 rel rates= 0.1118 subset rates= 0.0067) +pass 4 : -3351.0950 (branch= 0.0128 alpha= 0.0127 pinv= 0.0154 eq freqs= 0.0007 rel rates= 0.0949 subset rates= 0.0023) +pass 5 : -3350.9764 (branch= 0.0109 alpha= 0.0132 pinv= 0.0144 eq freqs= 0.0000 rel rates= 0.0768 subset rates= 0.0032) +pass 6 : -3350.8771 (branch= 0.0059 alpha= 0.0112 pinv= 0.0135 eq freqs= 0.0006 rel rates= 0.0657 subset rates= 0.0023) +pass 7 : -3350.7925 (branch= 0.0045 alpha= 0.0105 pinv= 0.0125 eq freqs= 0.0001 rel rates= 0.0559 subset rates= 0.0011) +pass 8 : -3350.7185 (branch= 0.0031 alpha= 0.0103 pinv= 0.0114 eq freqs= 0.0001 rel rates= 0.0481 subset rates= 0.0009) +pass 9 : -3350.6554 (branch= 0.0020 alpha= 0.0098 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0408 subset rates= 0.0000) +pass 10: -3350.5990 (branch= 0.0004 alpha= 0.0094 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0365 subset rates= 0.0000) +pass 11: -3350.5478 (branch= 0.0001 alpha= 0.0090 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0317 subset rates= 0.0012) +pass 12: -3350.5063 (branch= 0.0009 alpha= 0.0082 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0246 subset rates= 0.0000) +pass 13: -3350.4706 (branch= 0.0002 alpha= 0.0072 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0214 subset rates= 0.0000) +pass 14: -3350.4391 (branch= 0.0001 alpha= 0.0067 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0185 subset rates= 0.0000) +pass 15: -3350.4115 (branch= 0.0000 alpha= 0.0061 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0158 subset rates= 0.0000) +pass 16: -3350.3876 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0134 subset rates= 0.0000) +pass 17: -3350.3669 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0114 subset rates= 0.0000) +pass 18: -3350.3489 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0097 subset rates= 0.0000) +pass 19: -3350.3333 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0083 subset rates= 0.0000) +pass 20: -3350.3197 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0071 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2530 (branch= 0.0000 alpha= 0.0171 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.0340 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2378 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0079 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2343 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0021 subset rates= 0.0000) +pass 50: -3350.2344 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0020 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2336 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) +pass 60: -3350.2337 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 70: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 73: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 71: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2334 +Final score = -3350.2335 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.112, AG = 10.402, AT = 2.687, CG = 0.001, CT = 21.872, GT = 1.000 + AC = 3.113, AG = 10.408, AT = 2.688, CG = 0.001, CT = 21.882, 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 - 0.5784 + 0.5788 with an invariant (invariable) site category, proportion estimated - 0.3659 + 0.3661 Substitution rate categories under this model: rate proportion - 0.0000 0.3659 - 0.0487 0.1585 - 0.3001 0.1585 - 0.8699 0.1585 - 2.7814 0.1585 + 0.0000 0.3661 + 0.0488 0.1585 + 0.3003 0.1585 + 0.8701 0.1585 + 2.7808 0.1585 Model 2 Number of states = 2 (binary data) @@ -14421,13 +14457,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2334 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2335 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.112 10.4 2.687 0.001 21.87 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.113 10.41 2.688 0.001 21.88 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters @@ -14582,7 +14618,6 @@ 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 -300 -3324.3007 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14683,8 +14718,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 300, seed 1331320000, best lnL -3324.301 +Search rep 1 (of 2) generation 291, seed 1240487284, best lnL -3324.387 gen current_lnL precision last_tree_imp +291 -3324.3872 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 500 -3323.6818 0.500 1 @@ -14729,7 +14765,7 @@ pass 76: -3317.7870 (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 -Time used so far = 0 hours, 0 minutes and 49 seconds +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -14926,6 +14962,7 @@ 3800 -210.7083 0.010 1104 4000 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 +4400 -210.6492 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15005,33 +15042,38 @@ STARTING RUN Restarting from checkpoint... - generation 4362, seed 827780985, best lnL -210.650 + generation 4541, seed 1316982810, best lnL -210.648 gen current_lnL precision last_tree_imp -4362 -210.6496 0.010 1104 -4400 -210.6492 0.010 1104 -4500 -210.6477 0.010 1104 +4541 -210.6477 0.010 1104 +4600 -210.6257 0.010 1104 +4700 -210.6098 0.010 1104 +4800 -210.5948 0.010 1104 +4900 -210.5781 0.010 1104 +5000 -210.5740 0.010 1104 +5100 -210.5711 0.010 1104 +5200 -210.5693 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04689 +Improvement over last 500 gen = 0.04049 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.570, AG = 4.891, AT = 0.202, CG = 4.460, CT = 7.250, GT = 1.000 + AC = 2.798, AG = 5.234, AT = 0.196, CG = 4.937, CT = 7.823, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2331 0.3366 0.2107 0.2196 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.1902 + 1.2338 with an invariant (invariable) site category, proportion estimated - 0.1209 + 0.1337 Substitution rate categories under this model: rate proportion - 0.0000 0.1209 - 0.2293 0.2930 - 0.7543 0.2930 - 2.0164 0.2930 + 0.0000 0.1337 + 0.2378 0.2888 + 0.7623 0.2888 + 1.9999 0.2888 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -15042,15 +15084,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.6477 +Replicate 1 : -210.5693 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.57 4.891 0.2023 4.46 7.25 1 0.233 0.337 0.211 0.220 1.190 0.121 +rep 1: 2.798 5.234 0.1964 4.937 7.823 1 0.233 0.337 0.211 0.220 1.234 0.134 Treelengths: TL -rep 1: 2.247 +rep 1: 2.253 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 @@ -15192,9 +15234,6 @@ 4000 -165.9340 0.010 843 4200 -165.8876 0.010 843 4400 -165.8800 0.010 843 -4600 -165.7809 0.010 843 -4800 -165.7682 0.010 843 -5000 -165.6807 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15275,9 +15314,15 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 5107, seed 1750443106, best lnL -165.663 +Bootstrap rep 1 (of 1) generation 4595, seed 911553395, best lnL -165.781 gen current_lnL precision last_tree_imp -5107 -165.6632 0.010 843 +4595 -165.7813 0.010 843 +4600 -165.7809 0.010 843 +4700 -165.7799 0.010 843 +4800 -165.7682 0.010 843 +4900 -165.6827 0.010 843 +5000 -165.6807 0.010 843 +5100 -165.6632 0.010 843 5200 -165.6629 0.010 843 5300 -165.6249 0.010 843 5400 -165.5966 0.010 843 @@ -15324,36 +15369,32 @@ 9500 -163.5644 0.010 7573 9600 -163.5152 0.010 7573 9700 -163.4697 0.010 7573 -9800 -163.4652 0.010 7573 -9900 -163.4587 0.010 7573 -10000 -163.4575 0.010 7573 - Optimizing parameters... improved 1.431 lnL - Optimizing branchlengths... improved 0.011 lnL -NOTE: ****Specified generation limit (10000) reached... +NOTE: ****Specified time limit (5 seconds) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.785, AG = 10.721, AT = 2.714, CG = 4.252, CT = 44.709, GT = 1.000 + AC = 0.781, AG = 10.664, AT = 2.348, CG = 4.230, CT = 41.901, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1323 0.4184 0.2444 0.2049 + (ACGT) 0.1306 0.4191 0.2432 0.2072 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 38.8673 + 3.3607 with an invariant (invariable) site category, proportion estimated 0.3493 Substitution rate categories under this model: rate proportion 0.0000 0.3493 - 0.8041 0.1627 - 0.9408 0.1627 - 1.0445 0.1627 - 1.2106 0.1627 + 0.4154 0.1627 + 0.7497 0.1627 + 1.0838 0.1627 + 1.7511 0.1627 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. +>>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -15363,15 +15404,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -162.0150 +Replicate 1 : -163.4673 (TERMINATED PREMATURELY) Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.7854 10.72 2.714 4.252 44.71 1 0.132 0.418 0.244 0.205 38.867 0.349 +rep 1: 0.7813 10.66 2.348 4.23 41.9 1 0.131 0.419 0.243 0.207 3.361 0.349 Treelengths: TL -rep 1: 3.333 +rep 1: 3.264 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -15514,6 +15555,12 @@ 7200 -212.7020 0.010 3769 7400 -212.6750 0.010 3769 7600 -212.6702 0.010 3769 +7800 -212.6661 0.010 3769 +8000 -212.6646 0.010 3769 +8200 -212.6594 0.010 3769 +8400 -212.6591 0.010 3769 +8600 -212.6390 0.010 3769 +8800 -212.5865 0.010 3769 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15593,19 +15640,24 @@ STARTING RUN Restarting from checkpoint... - generation 7613, seed 1818039675, best lnL -212.670 + generation 8892, seed 701565579, best lnL -212.565 gen current_lnL precision last_tree_imp -7613 -212.6702 0.010 3769 -7700 -212.6690 0.010 3769 +8892 -212.5650 0.010 3769 +8900 -212.5650 0.010 3769 +9000 -212.5495 0.010 3769 +9100 -212.5424 0.010 3769 +9200 -212.5341 0.010 3769 +9300 -212.5317 0.010 3769 +9400 -212.5173 0.010 3769 Reached termination condition! last topological improvement at gen 3769 -Improvement over last 500 gen = 0.03303 +Improvement over last 500 gen = 0.04769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.420, AG = 10.376, AT = 0.430, CG = 10.567, CT = 6.838, GT = 1.000 + AC = 7.541, AG = 14.334, AT = 0.626, CG = 14.441, CT = 9.342, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2205 0.2887 0.1831 0.3078 Rate Heterogeneity Model: @@ -15620,15 +15672,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.6690 +Replicate 1 : -212.5173 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 5.42 10.38 0.4295 10.57 6.838 1 0.220 0.289 0.183 0.308 +rep 1: 7.541 14.33 0.6258 14.44 9.342 1 0.220 0.289 0.183 0.308 Treelengths: TL -rep 1: 1.730 +rep 1: 1.727 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 @@ -15867,9 +15919,10 @@ STARTING RUN Restarting from checkpoint... - generation 5917, seed 1995061465, best lnL -210.364 + generation 5856, seed 1041226720, best lnL -210.365 gen current_lnL precision last_tree_imp -5917 -210.3637 0.010 2883 +5856 -210.3648 0.010 2883 +5900 -210.3639 0.010 2883 6000 -210.3408 0.010 2883 6100 -210.3320 0.010 2883 6200 -210.3319 0.010 2883 @@ -16248,9 +16301,9 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 575, seed 830766625, best lnL -13371.208 +Bootstrap rep 1 (of 1) generation 545, seed 1254929279, best lnL -13371.274 gen current_lnL precision last_tree_imp -575 -13371.2075 0.402 0 +545 -13371.2736 0.402 0 600 -13371.2064 0.402 0 700 -13371.0754 0.402 0 800 -13370.9489 0.402 0 @@ -16546,6 +16599,108 @@ 3400 -467.7165 0.010 76 3500 -467.7162 0.010 76 3600 -467.7160 0.010 76 +3700 -467.7160 0.010 76 +3800 -467.7159 0.010 76 +Reached termination condition! +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00059 +Current score = -467.7159 +Performing final optimizations... +pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) +pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) +pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) +pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) +pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) +pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6783 (branch= 0.0000 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) +Looking for minimum length branches... +Final score = -467.6782 +Time used so far = 0 hours, 0 minutes and 5 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk 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 Mk 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 Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.79 1.48 2.18 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (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 (standard data) + Character change matrix: + One rate (symmetric one rate Mk 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 Mk 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 Mk 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=1831048457 + +Initial ln Likelihood: -637.1584 +optimizing: starting branch lengths, subset rates... +pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) +pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) +pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) +pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8409 +gen current_lnL precision last_tree_imp +0 -467.8409 0.010 0 +100 -467.8006 0.010 88 +200 -467.7829 0.010 88 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16671,111 +16826,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3666, seed 142632099, best lnL -467.716 +Search rep 2 (of 5) generation 235, seed 1649392380, best lnL -467.777 gen current_lnL precision last_tree_imp -3666 -467.7160 0.010 76 -3700 -467.7160 0.010 76 -3800 -467.7159 0.010 76 -Reached termination condition! -last topological improvement at gen 76 -Improvement over last 500 gen = 0.00059 -Current score = -467.7159 -Performing final optimizations... -pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) -pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) -pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) -pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) -pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0000 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) -Looking for minimum length branches... -Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 6 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk 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 Mk 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 Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.48 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (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 (standard data) - Character change matrix: - One rate (symmetric one rate Mk 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 Mk 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 Mk 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=1831048457 - -Initial ln Likelihood: -637.1584 -optimizing: starting branch lengths, subset rates... -pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) -pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) -pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) -pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8409 -gen current_lnL precision last_tree_imp -0 -467.8409 0.010 0 -100 -467.8006 0.010 88 -200 -467.7829 0.010 88 +235 -467.7772 0.010 88 300 -467.7645 0.010 88 400 -467.7572 0.010 88 500 -467.7508 0.010 88 @@ -16824,7 +16877,7 @@ pass 14: -467.6787 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6787 -Time used so far = 0 hours, 0 minutes and 10 seconds +Time used so far = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16906,28 +16959,35 @@ 400 -467.7649 0.010 0 500 -467.7557 0.010 0 600 -467.7482 0.010 0 +700 -467.7383 0.010 0 +800 -467.7308 0.010 0 +900 -467.7283 0.010 0 +1000 -467.7269 0.010 0 +1100 -467.7258 0.010 0 +1200 -467.7235 0.010 0 +1300 -467.7213 0.010 0 +1400 -467.7173 0.010 0 +1500 -467.7162 0.010 0 +1600 -467.7145 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7468 +Current score = -467.7145 Performing final optimizations... -pass 1 : -467.7464 (branch= 0.0000 subset rates= 0.0004) -pass 2 : -467.7233 (branch= 0.0218 subset rates= 0.0013) -pass 3 : -467.7104 (branch= 0.0124 subset rates= 0.0005) -pass 4 : -467.6938 (branch= 0.0166 subset rates= 0.0000) -pass 5 : -467.6863 (branch= 0.0074 subset rates= 0.0000) -pass 6 : -467.6827 (branch= 0.0037 subset rates= 0.0000) -pass 7 : -467.6812 (branch= 0.0015 subset rates= 0.0000) -pass 8 : -467.6805 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6791 (branch= 0.0004 subset rates= 0.0011) -pass 10: -467.6788 (branch= 0.0003 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 1 : -467.7132 (branch= 0.0000 subset rates= 0.0013) +pass 2 : -467.7012 (branch= 0.0119 subset rates= 0.0001) +pass 3 : -467.6974 (branch= 0.0039 subset rates= 0.0000) +pass 4 : -467.6910 (branch= 0.0064 subset rates= 0.0000) +pass 5 : -467.6862 (branch= 0.0048 subset rates= 0.0000) +pass 6 : -467.6827 (branch= 0.0035 subset rates= 0.0000) +pass 7 : -467.6806 (branch= 0.0009 subset rates= 0.0012) +pass 8 : -467.6793 (branch= 0.0013 subset rates= 0.0000) +pass 9 : -467.6788 (branch= 0.0005 subset rates= 0.0000) +pass 10: -467.6786 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6785 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6785 (branch= 0.0001 subset rates= 0.0000) pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0001) -pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 16: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 17: -467.6783 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6783 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16956,7 +17016,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.19 + 0.78 1.48 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16975,7 +17035,7 @@ Results: Replicate 1 : -467.6782 (best) Replicate 2 : -467.6787 (same topology as 1) -Replicate 3 : -467.6783 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6784 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16992,7 +17052,7 @@ TL R(1) R(2) R(3) rep 1: 3.844 0.786 1.480 2.180 rep 2: 3.839 0.788 1.472 2.178 -rep 3: 3.845 0.785 1.482 2.188 +rep 3: 3.845 0.785 1.483 2.186 Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### @@ -17209,7 +17269,7 @@ pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17292,6 +17352,9 @@ 300 -477.7486 0.010 74 400 -477.7424 0.010 74 500 -477.7295 0.010 74 +600 -477.7267 0.010 74 +700 -477.7205 0.010 74 +800 -477.7194 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17417,12 +17480,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 512, seed 942611345, best lnL -477.729 +Search rep 2 (of 5) generation 842, seed 729291124, best lnL -477.719 gen current_lnL precision last_tree_imp -512 -477.7295 0.010 74 -600 -477.7267 0.010 74 -700 -477.7205 0.010 74 -800 -477.7194 0.010 74 +842 -477.7189 0.010 74 900 -477.7186 0.010 74 1000 -477.7135 0.010 74 1100 -477.7094 0.010 74 @@ -17455,25 +17515,133 @@ 3800 -477.3085 0.010 2170 3900 -477.3085 0.010 2170 4000 -477.3085 0.010 2170 +4100 -477.3082 0.010 2170 +4200 -477.3082 0.010 2170 +4300 -477.3079 0.010 2170 +Reached termination condition! +last topological improvement at gen 2170 +Improvement over last 500 gen = 0.00067 +Current score = -477.3079 +Performing final optimizations... +pass 1 : -477.2447 (branch= 0.0000 subset rates= 0.0632) +pass 2 : -477.2336 (branch= 0.0111 subset rates= 0.0000) +pass 3 : -477.2150 (branch= 0.0106 subset rates= 0.0080) +pass 4 : -477.2129 (branch= 0.0020 subset rates= 0.0000) +pass 5 : -477.2082 (branch= 0.0047 subset rates= 0.0000) +pass 6 : -477.2060 (branch= 0.0019 subset rates= 0.0003) +pass 7 : -477.2056 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -477.2049 (branch= 0.0006 subset rates= 0.0001) +pass 9 : -477.2047 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2046 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2045 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.2045 +Time used so far = 0 hours, 0 minutes and 11 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 Mk 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 Mk 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 Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.64 1.93 2.63 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 2 (of 5)<<< + +>>>Search rep 3 (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 Mk 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 Mk 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 Mk 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=1602142636 + +Initial ln Likelihood: -662.4976 +optimizing: starting branch lengths, subset rates... +pass 1:+ 159.344 (branch= 147.93 scale= 1.33 subset rates= 10.09) +pass 2:+ 18.362 (branch= 14.32 scale= 0.01 subset rates= 4.02) +pass 3:+ 5.723 (branch= 4.51 scale= 0.00 subset rates= 1.22) +pass 4:+ 1.012 (branch= 0.74 scale= 0.00 subset rates= 0.28) +pass 5:+ 0.186 (branch= 0.17 scale= 0.00 subset rates= 0.02) +pass 6:+ 0.016 (branch= 0.00 scale= 0.02 subset rates= 0.00) +pass 7:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.8200 +gen current_lnL precision last_tree_imp +0 -477.8200 0.010 0 +100 -477.7127 0.010 12 +200 -477.6994 0.010 12 +300 -477.6923 0.010 12 +400 -477.5173 0.010 372 +500 -477.5116 0.010 372 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.3083 +Current score = -477.5090 Performing final optimizations... -pass 1 : -477.2363 (branch= 0.0000 subset rates= 0.0720) -pass 2 : -477.2259 (branch= 0.0085 subset rates= 0.0019) -pass 3 : -477.2158 (branch= 0.0101 subset rates= 0.0000) -pass 4 : -477.2121 (branch= 0.0037 subset rates= 0.0000) -pass 5 : -477.2076 (branch= 0.0041 subset rates= 0.0004) -pass 6 : -477.2061 (branch= 0.0015 subset rates= 0.0000) -pass 7 : -477.2052 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -477.2046 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -477.2044 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2043 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2043 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2043 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.2043 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.5078 (branch= 0.0002 subset rates= 0.0010) +pass 2 : -477.4713 (branch= 0.0364 subset rates= 0.0000) +pass 3 : -477.4552 (branch= 0.0148 subset rates= 0.0014) +pass 4 : -477.4420 (branch= 0.0131 subset rates= 0.0000) +pass 5 : -477.4380 (branch= 0.0040 subset rates= 0.0000) +pass 6 : -477.4357 (branch= 0.0023 subset rates= 0.0000) +pass 7 : -477.4342 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -477.4334 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -477.4324 (branch= 0.0004 subset rates= 0.0006) +pass 10: -477.4320 (branch= 0.0004 subset rates= 0.0000) +pass 11: -477.4318 (branch= 0.0002 subset rates= 0.0001) +pass 12: -477.4317 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2043 +Final score = -477.4315 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17502,11 +17670,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.94 2.63 + 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 2 (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!*** @@ -17514,13 +17682,14 @@ ####################################################### -Completed 2 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 : -477.4316 -Replicate 2 : -477.2043 (best) (TERMINATED PREMATURELY) +Replicate 2 : -477.2045 (best) +Replicate 3 : -477.4315 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17536,7 +17705,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.917 2.740 -rep 2: 4.697 0.635 1.937 2.629 +rep 2: 4.695 0.635 1.931 2.634 +rep 3: 4.928 0.632 1.914 2.740 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### @@ -17739,6 +17909,79 @@ 3300 -425.5851 0.010 365 3400 -425.5828 0.010 365 3500 -425.5828 0.010 365 +3600 -425.5827 0.010 365 +3700 -425.5827 0.010 365 +3800 -425.5826 0.010 365 +3900 -425.5824 0.010 365 +Reached termination condition! +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00046 +Current score = -425.5824 +Performing final optimizations... +pass 1 : -425.5752 (branch= 0.0000 subset rates= 0.0071) +pass 2 : -425.5571 (branch= 0.0147 subset rates= 0.0034) +pass 3 : -425.5512 (branch= 0.0059 subset rates= 0.0000) +pass 4 : -425.5505 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.5501 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.5497 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.5486 +Time used so far = 0 hours, 0 minutes and 5 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: + 0.87 1.53 1.12 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=255600397 + +Initial ln Likelihood: -577.2924 +optimizing: starting branch lengths, subset rates... +pass 1:+ 121.000 (branch= 120.23 scale= 0.75 subset rates= 0.02) +pass 2:+ 14.984 (branch= 14.74 scale= 0.04 subset rates= 0.20) +pass 3:+ 1.951 (branch= 1.90 scale= 0.00 subset rates= 0.05) +pass 4:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.3118 +gen current_lnL precision last_tree_imp +0 -439.3118 0.010 0 +100 -428.8361 0.010 97 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17867,34 +18110,67 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3583, seed 1464255224, best lnL -425.583 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 187, seed 1303855067, best lnL -428.043 gen current_lnL precision last_tree_imp -3583 -425.5827 0.010 365 -3600 -425.5827 0.010 365 -3700 -425.5827 0.010 365 -3800 -425.5826 0.010 365 -3900 -425.5824 0.010 365 +187 -428.0429 0.010 163 +200 -428.0348 0.010 163 +300 -425.9017 0.010 248 +400 -425.7902 0.010 327 +500 -425.7309 0.010 411 +600 -425.6571 0.010 523 +700 -425.6380 0.010 523 +800 -425.6343 0.010 523 +900 -425.6312 0.010 523 +1000 -425.6253 0.010 523 +1100 -425.6236 0.010 523 +1200 -425.6180 0.010 523 +1300 -425.6157 0.010 523 +1400 -425.6057 0.010 523 +1500 -425.6031 0.010 523 +1600 -425.5999 0.010 523 +1700 -425.5980 0.010 523 +1800 -425.5977 0.010 523 +1900 -425.5940 0.010 523 +2000 -425.5929 0.010 523 +2100 -425.5928 0.010 523 +2200 -425.5912 0.010 523 +2300 -425.5897 0.010 523 +2400 -425.5887 0.010 523 +2500 -425.5882 0.010 523 +2600 -425.5881 0.010 523 +2700 -425.5867 0.010 523 +2800 -425.5863 0.010 523 +2900 -425.5863 0.010 523 +3000 -425.5854 0.010 523 +3100 -425.5849 0.010 523 +3200 -425.5846 0.010 523 +3300 -425.5838 0.010 523 +3400 -425.5835 0.010 523 +3500 -425.5835 0.010 523 +3600 -425.5834 0.010 523 +3700 -425.5834 0.010 523 +3800 -425.5830 0.010 523 Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00046 -Current score = -425.5824 +last topological improvement at gen 523 +Improvement over last 500 gen = 0.00079 +Current score = -425.5830 Performing final optimizations... -pass 1 : -425.5752 (branch= 0.0000 subset rates= 0.0071) -pass 2 : -425.5571 (branch= 0.0147 subset rates= 0.0034) -pass 3 : -425.5512 (branch= 0.0059 subset rates= 0.0000) -pass 4 : -425.5505 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5501 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -425.5497 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.5767 (branch= 0.0000 subset rates= 0.0062) +pass 2 : -425.5554 (branch= 0.0187 subset rates= 0.0026) +pass 3 : -425.5554 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -425.5514 (branch= 0.0021 subset rates= 0.0019) +pass 5 : -425.5509 (branch= 0.0005 subset rates= 0.0000) +pass 6 : -425.5500 (branch= 0.0009 subset rates= 0.0000) +pass 7 : -425.5494 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -425.5492 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -425.5489 (branch= 0.0000 subset rates= 0.0003) +pass 10: -425.5488 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 6 seconds +Final score = -425.5487 +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17926,72 +18202,46 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=255600397 +Starting with seed=124386023 -Initial ln Likelihood: -577.2924 +Initial ln Likelihood: -667.8582 optimizing: starting branch lengths, subset rates... -pass 1:+ 121.000 (branch= 120.23 scale= 0.75 subset rates= 0.02) -pass 2:+ 14.984 (branch= 14.74 scale= 0.04 subset rates= 0.20) -pass 3:+ 1.951 (branch= 1.90 scale= 0.00 subset rates= 0.05) -pass 4:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.3118 +pass 1:+ 210.703 (branch= 209.92 scale= 0.77 subset rates= 0.01) +pass 2:+ 14.697 (branch= 14.50 scale= 0.07 subset rates= 0.12) +pass 3:+ 2.972 (branch= 2.91 scale= 0.03 subset rates= 0.04) +pass 4:+ 0.250 (branch= 0.24 scale= 0.01 subset rates= 0.00) +pass 5:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2013 gen current_lnL precision last_tree_imp -0 -439.3118 0.010 0 -100 -428.8361 0.010 97 -200 -428.0348 0.010 163 -300 -425.9017 0.010 248 -400 -425.7902 0.010 327 -500 -425.7309 0.010 411 -600 -425.6571 0.010 523 -700 -425.6380 0.010 523 -800 -425.6343 0.010 523 -900 -425.6312 0.010 523 -1000 -425.6253 0.010 523 -1100 -425.6236 0.010 523 -1200 -425.6180 0.010 523 -1300 -425.6157 0.010 523 -1400 -425.6057 0.010 523 -1500 -425.6031 0.010 523 -1600 -425.5999 0.010 523 -1700 -425.5980 0.010 523 -1800 -425.5977 0.010 523 -1900 -425.5940 0.010 523 -2000 -425.5929 0.010 523 -2100 -425.5928 0.010 523 -2200 -425.5912 0.010 523 -2300 -425.5897 0.010 523 -2400 -425.5887 0.010 523 -2500 -425.5882 0.010 523 -2600 -425.5881 0.010 523 -2700 -425.5867 0.010 523 -2800 -425.5863 0.010 523 -2900 -425.5863 0.010 523 -3000 -425.5854 0.010 523 -3100 -425.5849 0.010 523 -3200 -425.5846 0.010 523 +0 -439.2013 0.010 0 +100 -429.9526 0.010 95 +200 -428.0661 0.010 184 +300 -425.6075 0.010 283 +400 -425.4842 0.010 312 +500 -425.4465 0.010 472 +600 -425.4348 0.010 472 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.5838 +Current score = -425.4283 Performing final optimizations... -pass 1 : -425.5805 (branch= 0.0000 subset rates= 0.0033) -pass 2 : -425.5548 (branch= 0.0189 subset rates= 0.0068) -pass 3 : -425.5531 (branch= 0.0013 subset rates= 0.0004) -pass 4 : -425.5522 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -425.5517 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -425.5501 (branch= 0.0016 subset rates= 0.0000) -pass 7 : -425.5497 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0003) -pass 9 : -425.5488 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3804 (branch= 0.0425 subset rates= 0.0054) +pass 2 : -425.3511 (branch= 0.0293 subset rates= 0.0000) +pass 3 : -425.3315 (branch= 0.0197 subset rates= 0.0000) +pass 4 : -425.3271 (branch= 0.0044 subset rates= 0.0000) +pass 5 : -425.3228 (branch= 0.0043 subset rates= 0.0000) +pass 6 : -425.3211 (branch= 0.0016 subset rates= 0.0000) +pass 7 : -425.3208 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -425.3206 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -425.3205 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3205 (branch= 0.0001 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) Looking for minimum length branches... -Final score = -425.5487 +Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18020,11 +18270,11 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.13 + 0.86 1.54 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) 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!*** @@ -18032,13 +18282,14 @@ ####################################################### -Completed 2 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 : -425.5486 (best) -Replicate 2 : -425.5487 (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 +Replicate 2 : -425.5487 (same topology as 1) +Replicate 3 : -425.3204 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18054,10 +18305,12 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.037 0.868 1.530 1.116 -rep 2: 3.037 0.868 1.529 1.125 +rep 2: 3.039 0.869 1.526 1.120 +rep 3: 2.979 0.865 1.539 1.148 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -18248,6 +18501,109 @@ 2500 -473.9804 0.010 653 2600 -473.9801 0.010 653 2700 -473.9793 0.010 653 +2800 -473.9779 0.010 653 +2900 -473.9777 0.010 653 +3000 -473.9777 0.010 653 +3100 -473.9773 0.010 653 +3200 -473.9772 0.010 653 +3300 -473.9770 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9770 +Performing final optimizations... +pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) +pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) +pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) +pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) +pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 5 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 2.07 2.80 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (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=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8071 +gen current_lnL precision last_tree_imp +0 -474.8071 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18373,112 +18729,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2707, seed 1357814324, best lnL -473.979 -gen current_lnL precision last_tree_imp -2707 -473.9793 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9777 0.010 653 -3000 -473.9777 0.010 653 -3100 -473.9773 0.010 653 -3200 -473.9772 0.010 653 -3300 -473.9770 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00088 -Current score = -473.9770 -Performing final optimizations... -pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) -pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) -pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) -pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) -pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 7 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 2.07 2.80 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (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=2125680066 - -Initial ln Likelihood: -649.8224 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) -pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) -pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) -pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) -pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8071 +Search rep 2 (of 5) generation 12, seed 1384067187, best lnL -474.802 gen current_lnL precision last_tree_imp -0 -474.8071 0.010 0 +12 -474.8016 0.010 0 100 -474.7912 0.010 0 200 -474.7021 0.010 123 300 -474.5642 0.010 272 @@ -18503,28 +18756,39 @@ 2200 -474.4775 0.010 272 2300 -474.4768 0.010 272 2400 -474.4764 0.010 272 +2500 -474.4764 0.010 272 +2600 -474.4747 0.010 272 +2700 -474.4736 0.010 272 +2800 -474.4720 0.010 272 +2900 -474.4720 0.010 272 +3000 -474.4652 0.010 272 +3100 -474.4597 0.010 272 +3200 -474.4561 0.010 272 +3300 -474.4551 0.010 272 +3400 -474.4539 0.010 272 +3500 -474.4525 0.010 272 +3600 -474.4521 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4764 +Current score = -474.4521 Performing final optimizations... -pass 1 : -474.4686 (branch= 0.0078 subset rates= 0.0000) -pass 2 : -474.4448 (branch= 0.0238 subset rates= 0.0000) -pass 3 : -474.4366 (branch= 0.0082 subset rates= 0.0000) -pass 4 : -474.4351 (branch= 0.0015 subset rates= 0.0000) -pass 5 : -474.4332 (branch= 0.0018 subset rates= 0.0000) -pass 6 : -474.4310 (branch= 0.0022 subset rates= 0.0000) -pass 7 : -474.4302 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -474.4298 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -474.4295 (branch= 0.0003 subset rates= 0.0000) -pass 10: -474.4294 (branch= 0.0001 subset rates= 0.0000) -pass 11: -474.4293 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4292 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.4286 (branch= 0.0000 subset rates= 0.0006) -pass 14: -474.4285 (branch= 0.0001 subset rates= 0.0001) -pass 15: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 17: -474.4284 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4521 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -474.4428 (branch= 0.0092 subset rates= 0.0000) +pass 3 : -474.4359 (branch= 0.0070 subset rates= 0.0000) +pass 4 : -474.4322 (branch= 0.0036 subset rates= 0.0001) +pass 5 : -474.4306 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -474.4300 (branch= 0.0006 subset rates= 0.0000) +pass 7 : -474.4295 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -474.4291 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -474.4287 (branch= 0.0004 subset rates= 0.0000) +pass 10: -474.4284 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4283 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 16: -474.4282 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4284 +Final score = -474.4282 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18553,7 +18817,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.91 + 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -18571,7 +18835,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9507 (best) -Replicate 2 : -474.4284 (TERMINATED PREMATURELY) +Replicate 2 : -474.4282 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18587,7 +18851,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.066 2.804 -rep 2: 4.598 0.589 2.032 2.907 +rep 2: 4.600 0.588 2.030 2.924 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -18605,7 +18869,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j3 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -18664,9 +18928,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-9_armhf.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_armhf.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-9_armhf.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_armhf.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_armhf.buildinfo @@ -18676,12 +18940,14 @@ 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/20841/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20841/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/1706 and its subdirectories -I: Current time: Sat Dec 21 01:22:00 -12 2024 -I: pbuilder-time-stamp: 1734787320 +I: removing directory /srv/workspace/pbuilder/20841 and its subdirectories +I: Current time: Sun Dec 22 03:36:04 +14 2024 +I: pbuilder-time-stamp: 1734788164