Diff of the two buildlogs: -- --- b1/build.log 2024-05-26 13:56:42.995893989 +0000 +++ b2/build.log 2024-05-26 14:01:17.252198825 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 28 08:15:21 -12 2025 -I: pbuilder-time-stamp: 1751141721 +I: Current time: Mon May 27 03:56:46 +14 2024 +I: pbuilder-time-stamp: 1716731806 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking garli_2.1-7.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1827889/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1086102/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 26 13:56 /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/1086102/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1086102/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='1bca9fea5e614b04b193d16e05f836fa' - 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='1827889' - PS1='# ' - PS2='> ' + INVOCATION_ID=eff734860b894892ac4160dbfe8146bd + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1086102 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.S3nTGUBs/pbuilderrc_8mKG --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.S3nTGUBs/b1 --logfile b1/build.log garli_2.1-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.S3nTGUBs/pbuilderrc_gi8T --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.S3nTGUBs/b2 --logfile b2/build.log garli_2.1-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 27 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1827889/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 25 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1086102/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -215,7 +247,7 @@ Get: 99 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 ncl-tools arm64 2.1.21+git20210811.b1213a7-5+b1 [188 kB] -Fetched 96.3 MB in 0s (195 MB/s) +Fetched 96.3 MB in 1s (142 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 ... 19763 files and directories currently installed.) @@ -641,7 +673,11 @@ 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_2.1-7_source.changes +I: user script /srv/workspace/pbuilder/1086102/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1086102/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_2.1-7_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-7 dpkg-buildpackage: info: source distribution unstable @@ -745,8 +781,8 @@ 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 @@ -833,38 +869,16 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -In file included from /usr/include/stdio.h:964, - from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': +linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1322 | register int nsq = n * n; + | ^~~ In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -909,36 +923,43 @@ /usr/include/c++/13/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 file included from /usr/include/stdio.h:964, + from /usr/include/c++/13/cstdio:42, + from /usr/include/c++/13/ext/string_conversions.h:45, + from /usr/include/c++/13/bits/basic_string.h:4109, + from /usr/include/c++/13/string:54, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from individual.cpp:28: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from configreader.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -976,9 +997,15 @@ /usr/include/c++/13/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{ | ^~~~~~~~~~~~~~~ @@ -988,7 +1015,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from model.cpp:17: + from population.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1033,8 +1060,7 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from adaptation.cpp:25: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1044,7 +1070,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1082,11 +1108,30 @@ /usr/include/c++/13/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{ | ^~~~~~~~~~~~~~~ @@ -1096,7 +1141,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from configreader.cpp:21: + from model.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1134,15 +1179,12 @@ /usr/include/c++/13/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{ | ^~~~~~~~~~~~~~~ @@ -1152,7 +1194,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from population.h:23: + from adaptation.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1194,25 +1236,19 @@ 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from population.h:23: + from /usr/include/c++/13/iomanip:42, + from individual.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1250,12 +1286,18 @@ /usr/include/c++/13/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] @@ -1375,49 +1453,20 @@ 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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:964, + from configreader.cpp:18: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1496,7 +1545,9 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from datamatr.cpp:20: + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1508,34 +1559,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'void Population::RunTests()': -population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -1556,7 +1579,13 @@ from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54: + from /usr/include/c++/13/string:54, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1599,50 +1628,13 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:964, - from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:964, - from configreader.cpp:18: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: + from /usr/include/c++/13/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1658,14 +1650,7 @@ from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from rng.h:36, - from tree.h:30: + from /usr/include/c++/13/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1677,40 +1662,36 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'void Population::RunTests()': +population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': +reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 388 | fread(&unique, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +reconnode.h: In constructor 'Swap::Swap(FILE*&)': +reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 264 | fread(&count, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from treenode.h:30, + from tree.h:31: +bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': +bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': +population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1880 | fread((char *) &seed, sizeof(seed), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1887 | fread((char *) &t, sizeof(t), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(this, scalarSize, 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); - | ~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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, @@ -1788,7 +1769,13 @@ from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54, - from population.cpp:25: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1800,64 +1787,42 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] + 323 | else sprintf(temp, ".run%d", rank); + | ^~ +garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] + 323 | else sprintf(temp, ".run%d", rank); + | ^~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); + | ~~~~~~~~~~~~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~ +garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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 ()); + | ~~~~~~~~~~~~~~~~~ tree.cpp: In member function 'std::pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': 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++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/map:62, - from /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, - from /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:2911, - from mpitrick.cpp:20: -/usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438: -/usr/include/c++/13/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++/13/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++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/map:62, + from /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, + from /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:2911, + from mpitrick.cpp:20: +/usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438: +/usr/include/c++/13/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++/13/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++/13/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from population.h:23: -/usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438: -/usr/include/c++/13/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++/13/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++/13/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from model.cpp:26: + from funcs.h:25, + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2364,7 +2351,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from model.cpp:17: + from adaptation.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2402,21 +2389,24 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from population.h:23: + from /usr/include/c++/13/iomanip:42, + from individual.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2447,6 +2437,10 @@ /usr/include/c++/13/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 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; @@ -2458,15 +2452,6 @@ 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from model.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2533,15 +2518,11 @@ /usr/include/c++/13/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{ | ^~~~~~~~~~~~~~~ @@ -2551,7 +2532,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2589,59 +2570,11 @@ /usr/include/c++/13/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++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from population.h:23: +/usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1438: +/usr/include/c++/13/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++/13/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++/13/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] @@ -2758,6 +2757,42 @@ 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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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, @@ -2805,19 +2840,6 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from /usr/include/stdio.h:964, - from configreader.cpp:18: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -2825,9 +2847,8 @@ | ^ In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54: + 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2839,6 +2860,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -2862,6 +2884,35 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'void Population::RunTests()': +population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': +reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 388 | fread(&unique, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +reconnode.h: In constructor 'Swap::Swap(FILE*&)': +reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 264 | fread(&count, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from treenode.h:30, + from tree.h:31: +bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': +bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': +population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1880 | fread((char *) &seed, sizeof(seed), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1887 | fread((char *) &t, sizeof(t), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(this, scalarSize, 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -2878,6 +2929,18 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:964, + from configreader.cpp:18: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, @@ -2927,17 +2990,14 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from datamatr.cpp:20: + from /usr/include/c++/13/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2949,41 +3009,17 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -population.cpp: In member function 'void Population::RunTests()': -population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: + from /usr/include/c++/13/ext/string_conversions.h:45, + from /usr/include/c++/13/bits/basic_string.h:4109, + from /usr/include/c++/13/string:54, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2995,7 +3031,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -3019,6 +3054,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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, @@ -3061,6 +3097,23 @@ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /usr/include/stdio.h:964, + from /usr/include/c++/13/cstdio:42, + from /usr/include/c++/13/ext/string_conversions.h:45, + from /usr/include/c++/13/bits/basic_string.h:4109, + from /usr/include/c++/13/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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ 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; @@ -3068,22 +3121,14 @@ /usr/include/c++/13/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 Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': -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){ - | ^ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3095,6 +3140,14 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': +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){ + | ^ 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); @@ -3162,30 +3215,33 @@ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:964, - from /usr/include/c++/13/cstdio:42, - from /usr/include/c++/13/ext/string_conversions.h:45, - from /usr/include/c++/13/bits/basic_string.h:4109, - from /usr/include/c++/13/string:54, - from population.cpp:25: +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 2147483647] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 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 ()); | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54, - from translatetable.h:24, - from translatetable.cpp:19: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3202,12 +3258,8 @@ from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from treenode.cpp:21: + from translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3219,22 +3271,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 2147483647] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 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 /usr/include/stdio.h:964, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, @@ -5790,7 +5826,7 @@ pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5940,7 +5976,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6389,7 +6425,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 5 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6593,7 +6629,7 @@ pass 75: -3350.2333 (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 = -3350.2333 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6801,7 +6837,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6963,7 +6999,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8810,7 +8846,7 @@ pass 15: -464.5474 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -464.5474 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -13422,9 +13458,6 @@ 1700 -110.2780 0.010 707 1800 -110.2329 0.010 707 1900 -110.2137 0.010 707 -2000 -110.1884 0.010 707 -2100 -110.1532 0.010 707 -2200 -110.1459 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13511,9 +13544,9 @@ STARTING RUN Restarting from checkpoint... - generation 2297, seed 1752233065, best lnL -110.135 + generation 1970, seed 865183624, best lnL -110.196 gen current_lnL precision last_tree_imp -2297 -110.1347 0.010 707 +1970 -110.1960 0.010 707 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13527,16 +13560,16 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 3.5916 + 2.9338 with an invariant (invariable) site category, proportion estimated - 0.1847 + 0.1544 Substitution rate categories under this model: rate proportion - 0.0000 0.1847 - 0.4304 0.2038 - 0.7598 0.2038 - 1.0842 0.2038 - 1.7256 0.2038 + 0.0000 0.1544 + 0.3841 0.2114 + 0.7278 0.2114 + 1.0822 0.2114 + 1.8060 0.2114 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -13547,15 +13580,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -110.1347 +Replicate 1 : -110.1960 Parameter estimates: alpha pinv -rep 1: 3.592 0.185 +rep 1: 2.934 0.154 Treelengths: TL -rep 1: 2.701 +rep 1: 2.692 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log @@ -14085,9 +14118,9 @@ STARTING RUN Restarting from checkpoint... - generation 205, seed 1596430740, best lnL -204.798 + generation 207, seed 1224585207, best lnL -204.798 gen current_lnL precision last_tree_imp -205 -204.7979 0.500 172 +207 -204.7979 0.500 172 MODEL REPORT - Parameter values are FINAL Model 1 @@ -14371,9 +14404,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 207, seed 1224585207, best lnL -194.241 +Bootstrap rep 1 (of 1) generation 208, seed 896699740, best lnL -194.241 gen current_lnL precision last_tree_imp -207 -194.2413 0.500 196 +208 -194.2413 0.500 196 MODEL REPORT - Parameter values are FINAL Model 1 @@ -14728,9 +14761,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 5468, seed 1935547454, best lnL -3350.710 +Search rep 1 (of 2) generation 5459, seed 1591439189, best lnL -3350.755 gen current_lnL precision last_tree_imp -5468 -3350.7098 0.010 0 +5459 -3350.7547 0.010 0 5500 -3350.7006 0.010 0 5600 -3350.6627 0.010 0 5700 -3350.6587 0.010 0 @@ -15043,7 +15076,6 @@ 1300 -3320.0846 0.010 1 1400 -3320.0682 0.010 1 1500 -3320.0214 0.010 1 -1600 -3320.0171 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15144,9 +15176,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1606, seed 169525534, best lnL -3320.017 +Search rep 1 (of 2) generation 1585, seed 539922908, best lnL -3320.017 gen current_lnL precision last_tree_imp -1606 -3320.0171 0.010 1 +1585 -3320.0171 0.010 1 +1600 -3320.0171 0.010 1 1700 -3320.0139 0.010 1 1800 -3319.8184 0.010 1 1900 -3319.6004 0.010 1 @@ -15159,63 +15192,61 @@ 2600 -3319.1410 0.010 1 2700 -3319.1330 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3319.1222 +Current score = -3319.1249 Performing final optimizations... -pass 1 : -3318.9241 (branch= 0.0116 alpha= 0.0000 pinv= 0.0161 eq freqs= 0.0062 rel rates= 0.1137 ins/del rates= 0.0505) -pass 2 : -3318.7598 (branch= 0.0374 alpha= 0.0055 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.0938 ins/del rates= 0.0116) -pass 3 : -3318.6247 (branch= 0.0260 alpha= 0.0104 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0762 ins/del rates= 0.0076) -pass 4 : -3318.5044 (branch= 0.0216 alpha= 0.0112 pinv= 0.0139 eq freqs= 0.0007 rel rates= 0.0658 ins/del rates= 0.0072) -pass 5 : -3318.4113 (branch= 0.0112 alpha= 0.0096 pinv= 0.0132 eq freqs= 0.0006 rel rates= 0.0538 ins/del rates= 0.0046) -pass 6 : -3318.3311 (branch= 0.0077 alpha= 0.0099 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0471 ins/del rates= 0.0031) -pass 7 : -3318.2613 (branch= 0.0050 alpha= 0.0095 pinv= 0.0114 eq freqs= 0.0003 rel rates= 0.0414 ins/del rates= 0.0020) -pass 8 : -3318.2015 (branch= 0.0034 alpha= 0.0095 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0351 ins/del rates= 0.0014) -pass 9 : -3318.1491 (branch= 0.0022 alpha= 0.0088 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0306 ins/del rates= 0.0009) -pass 10: -3318.1036 (branch= 0.0014 alpha= 0.0084 pinv= 0.0088 eq freqs= 0.0000 rel rates= 0.0262 ins/del rates= 0.0006) -pass 11: -3318.0638 (branch= 0.0009 alpha= 0.0078 pinv= 0.0080 eq freqs= 0.0000 rel rates= 0.0227 ins/del rates= 0.0004) -pass 12: -3318.0288 (branch= 0.0006 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0196 ins/del rates= 0.0003) -pass 13: -3317.9982 (branch= 0.0004 alpha= 0.0066 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0168 ins/del rates= 0.0002) -pass 14: -3317.9713 (branch= 0.0003 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0001) -pass 15: -3317.9478 (branch= 0.0002 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0125 ins/del rates= 0.0001) -pass 16: -3317.9271 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0108 ins/del rates= 0.0000) -pass 17: -3317.9090 (branch= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0093 ins/del rates= 0.0000) -pass 18: -3317.8932 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) -pass 19: -3317.8793 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) -pass 20: -3317.8671 (branch= 0.0000 alpha= 0.0032 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0060 ins/del rates= 0.0000) +pass 1 : -3318.9342 (branch= 0.0124 alpha= 0.0000 pinv= 0.0071 eq freqs= 0.0061 rel rates= 0.1140 ins/del rates= 0.0511) +pass 2 : -3318.7698 (branch= 0.0366 alpha= 0.0056 pinv= 0.0164 eq freqs= 0.0000 rel rates= 0.0945 ins/del rates= 0.0114) +pass 3 : -3318.6345 (branch= 0.0259 alpha= 0.0107 pinv= 0.0148 eq freqs= 0.0000 rel rates= 0.0763 ins/del rates= 0.0075) +pass 4 : -3318.5154 (branch= 0.0211 alpha= 0.0118 pinv= 0.0142 eq freqs= 0.0006 rel rates= 0.0643 ins/del rates= 0.0070) +pass 5 : -3318.4218 (branch= 0.0112 alpha= 0.0099 pinv= 0.0136 eq freqs= 0.0006 rel rates= 0.0538 ins/del rates= 0.0046) +pass 6 : -3318.3407 (branch= 0.0078 alpha= 0.0102 pinv= 0.0126 eq freqs= 0.0000 rel rates= 0.0473 ins/del rates= 0.0032) +pass 7 : -3318.2704 (branch= 0.0050 alpha= 0.0099 pinv= 0.0117 eq freqs= 0.0003 rel rates= 0.0413 ins/del rates= 0.0020) +pass 8 : -3318.2098 (branch= 0.0034 alpha= 0.0098 pinv= 0.0108 eq freqs= 0.0000 rel rates= 0.0352 ins/del rates= 0.0014) +pass 9 : -3318.1567 (branch= 0.0022 alpha= 0.0092 pinv= 0.0099 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0010) +pass 10: -3318.1105 (branch= 0.0015 alpha= 0.0087 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0262 ins/del rates= 0.0006) +pass 11: -3318.0700 (branch= 0.0010 alpha= 0.0081 pinv= 0.0083 eq freqs= 0.0000 rel rates= 0.0228 ins/del rates= 0.0004) +pass 12: -3318.0344 (branch= 0.0006 alpha= 0.0075 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0196 ins/del rates= 0.0003) +pass 13: -3318.0033 (branch= 0.0004 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0002) +pass 14: -3317.9759 (branch= 0.0003 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0001) +pass 15: -3317.9518 (branch= 0.0002 alpha= 0.0057 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0001) +pass 16: -3317.9308 (branch= 0.0001 alpha= 0.0052 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0108 ins/del rates= 0.0000) +pass 17: -3317.9122 (branch= 0.0001 alpha= 0.0047 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0094 ins/del rates= 0.0000) +pass 18: -3317.8960 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) +pass 19: -3317.8818 (branch= 0.0000 alpha= 0.0037 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) +pass 20: -3317.8694 (branch= 0.0000 alpha= 0.0033 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0061 ins/del rates= 0.0000) optimization up to ... -pass 30: -3317.8059 (branch= 0.0000 alpha= 0.0167 pinv= 0.0154 eq freqs= 0.0001 rel rates= 0.0291 ins/del rates= 0.0000) +pass 30: -3317.8064 (branch= 0.0000 alpha= 0.0176 pinv= 0.0161 eq freqs= 0.0001 rel rates= 0.0292 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7912 (branch= 0.0001 alpha= 0.0041 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) +pass 40: -3317.7913 (branch= 0.0001 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) optimization up to ... pass 50: -3317.7879 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0016 ins/del rates= 0.0000) optimization up to ... pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) - optimization up to ... -pass 71: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 66: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 +Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.069, AG = 10.274, AT = 2.659, CG = 0.001, CT = 21.566, GT = 1.000 + AC = 3.062, AG = 10.254, AT = 2.653, CG = 0.001, CT = 21.513, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1567 0.2882 + (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5746 + 0.5740 with an invariant (invariable) site category, proportion estimated - 0.3612 + 0.3610 Substitution rate categories under this model: rate proportion - 0.0000 0.3612 - 0.0479 0.1597 - 0.2979 0.1597 - 0.8678 0.1597 - 2.7864 0.1597 + 0.0000 0.3610 + 0.0478 0.1598 + 0.2975 0.1598 + 0.8675 0.1598 + 2.7872 0.1598 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15241,13 +15272,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.069 10.27 2.659 0.001 21.57 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.062 10.25 2.653 0.001 21.51 1 0.333 0.222 0.157 0.288 0.574 0.361 Partition model subset 2: ins del @@ -16816,7 +16847,6 @@ 3000 -13370.3644 0.010 0 3100 -13370.3583 0.010 0 3200 -13370.3526 0.010 0 -3300 -13370.3479 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16939,9 +16969,9 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3390, seed 268814297, best lnL -13370.348 +Bootstrap rep 1 (of 1) generation 3294, seed 1398859808, best lnL -13370.348 gen current_lnL precision last_tree_imp -3390 -13370.3478 0.010 0 +3294 -13370.3479 0.010 0 MODEL REPORT - Parameter values are FINAL Model 1 @@ -16965,7 +16995,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.623, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.623, GT = 1.000 + AC = 2.631, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.631, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2819 0.1752 0.1596 0.3832 Rate Heterogeneity Model: @@ -17008,7 +17038,7 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3478 +Replicate 1 : -13370.3479 Parameter estimates: @@ -17018,7 +17048,7 @@ Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.623 4.225 0.813 4.225 2.623 1 0.282 0.175 0.160 0.383 0.245 +rep 1: 2.631 4.225 0.813 4.225 2.631 1 0.282 0.175 0.160 0.383 0.245 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv @@ -17625,7 +17655,6 @@ 2900 -467.7074 0.010 0 3000 -467.7070 0.010 0 3100 -467.7067 0.010 0 -3200 -467.7066 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17751,9 +17780,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 4 (of 5) generation 3233, seed 1720093931, best lnL -467.707 +Search rep 4 (of 5) generation 3164, seed 197959835, best lnL -467.707 gen current_lnL precision last_tree_imp -3233 -467.7066 0.010 0 +3164 -467.7067 0.010 0 +3200 -467.7066 0.010 0 3300 -467.7066 0.010 0 3400 -467.7066 0.010 0 Reached termination condition! @@ -18462,8 +18492,6 @@ 2100 -477.6496 0.010 238 2200 -477.2798 0.010 2146 2300 -477.2675 0.010 2146 -2400 -477.2657 0.010 2146 -2500 -477.2640 0.010 2146 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18589,9 +18617,11 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 2538, seed 1334681995, best lnL -477.264 +Search rep 3 (of 5) generation 2357, seed 7430493, best lnL -477.266 gen current_lnL precision last_tree_imp -2538 -477.2639 0.010 2146 +2357 -477.2657 0.010 2146 +2400 -477.2657 0.010 2146 +2500 -477.2640 0.010 2146 2600 -477.2636 0.010 2146 2700 -477.2624 0.010 2146 2800 -477.2612 0.010 2146 @@ -19394,10 +19424,6 @@ 3100 -425.3459 0.010 611 3200 -425.3458 0.010 611 3300 -425.3455 0.010 611 -3400 -425.3443 0.010 611 -3500 -425.3443 0.010 611 -3600 -425.3438 0.010 611 -3700 -425.3437 0.010 611 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19526,9 +19552,13 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 3 (of 5) generation 3754, seed 1929912345, best lnL -425.344 +Bootstrap rep 1 (of 1) Search rep 3 (of 5) generation 3389, seed 1279553421, best lnL -425.344 gen current_lnL precision last_tree_imp -3754 -425.3437 0.010 611 +3389 -425.3444 0.010 611 +3400 -425.3443 0.010 611 +3500 -425.3443 0.010 611 +3600 -425.3438 0.010 611 +3700 -425.3437 0.010 611 3800 -425.3436 0.010 611 3900 -425.3433 0.010 611 4000 -425.3433 0.010 611 @@ -20216,7 +20246,7 @@ pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4281 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20313,11 +20343,6 @@ 1800 -474.4894 0.010 474 1900 -474.4887 0.010 474 2000 -474.4853 0.010 474 -2100 -474.4846 0.010 474 -2200 -474.4834 0.010 474 -2300 -474.4828 0.010 474 -2400 -474.4825 0.010 474 -2500 -474.4819 0.010 474 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -20443,9 +20468,14 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 2538, seed 1484597303, best lnL -474.482 +Search rep 3 (of 5) generation 2035, seed 1982394253, best lnL -474.485 gen current_lnL precision last_tree_imp -2538 -474.4815 0.010 474 +2035 -474.4851 0.010 474 +2100 -474.4846 0.010 474 +2200 -474.4834 0.010 474 +2300 -474.4828 0.010 474 +2400 -474.4825 0.010 474 +2500 -474.4819 0.010 474 2600 -474.4804 0.010 474 2700 -474.4799 0.010 474 2800 -474.4775 0.010 474 @@ -20915,10 +20945,10 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_arm64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_arm64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-7_arm64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_arm64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_arm64.deb'. -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_arm64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_arm64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_arm64.changes @@ -20927,12 +20957,14 @@ 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/1086102/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1086102/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/1827889 and its subdirectories -I: Current time: Sat Jun 28 08:19:40 -12 2025 -I: pbuilder-time-stamp: 1751141980 +I: removing directory /srv/workspace/pbuilder/1086102 and its subdirectories +I: Current time: Mon May 27 04:01:16 +14 2024 +I: pbuilder-time-stamp: 1716732076