Diff of the two buildlogs: -- --- b1/build.log 2024-05-22 04:14:58.713499396 +0000 +++ b2/build.log 2024-05-22 04:46:52.616156112 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 21 16:04:25 -12 2024 -I: pbuilder-time-stamp: 1716350665 +I: Current time: Wed May 22 18:16:17 +14 2024 +I: pbuilder-time-stamp: 1716351377 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/25552/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2336/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4a. +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 22 04:16 /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/2336/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2336/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='70a4eb93258146c6a427791c3de79b37' - 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='25552' - PS1='# ' - PS2='> ' + INVOCATION_ID=9752cbda81844da596eb0930978c2c0a + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2336 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.9rrUerns/pbuilderrc_ZISb --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9rrUerns/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9rrUerns/pbuilderrc_wYTz --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9rrUerns/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-armmp #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 19 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/25552/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 21 11:26 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2336/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -150,7 +182,7 @@ Get: 34 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] -Fetched 19.4 MB in 0s (44.7 MB/s) +Fetched 19.4 MB in 1s (14.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19446 files and directories currently installed.) @@ -309,7 +341,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && 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 > ../plink_1.07+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/2336/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2336/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && 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 > ../plink_1.07+dfsg-4_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -321,7 +357,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' @@ -336,26 +372,52 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 - make -j3 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 + make -j4 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from input.cpp:24: +In file included from binput.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from plink.cpp:28: +In file included from input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +binput.cpp: In member function 'void Plink::readBinData()': +binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 261 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 339 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 351 | while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 516 | if ( i == include.size() ) @@ -382,6 +444,11 @@ input.cpp:695:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 695 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 787 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1064 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1208 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from plink.cpp:40: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 2471 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 2366 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -binput.cpp: In member function 'void Plink::readBinData()': -binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 157 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 176 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 186 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 261 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 339 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/algorithm:61, - from input.cpp:18: -/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2649 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/algorithm:61, from binput.cpp:19: /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -583,83 +608,18 @@ /usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2401 | __merge_adaptive(_BidirectionalIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2401 | __merge_adaptive(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2716 | __merge_sort_with_buffer(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2727:34: -/usr/include/c++/13/bits/stl_algo.h:2706:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2706 | std::__insertion_sort(__first, __first + __chunk_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2709:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2709 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2709:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator >; _RandomAccessIterator2 = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2731:26: -/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2684 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2685 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2687 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2692 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2693 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = Locus*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2734:26: -/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2684 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2685 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2687 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2692 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2693 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1283 | __rotate(_RandomAccessIterator __first, - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2716 | __merge_sort_with_buffer(_RandomAccessIterator __first, @@ -1061,6 +1021,39 @@ | ~~~~~~~~~~~~~~~~~~ 2799 | __comp); | ~~~~~~~ +In file included from tinput.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +tinput.cpp: In member function 'void Plink::readTransposedData()': +tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 309 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 591 | if ( c > sample.size()) + | ~~^~~~~~~~~~~~~~~ +tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:69: /usr/include/c++/13/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1079,13 +1072,6 @@ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1400 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from plink.h:21, - from input.cpp:23: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive_resize(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2424 | __merge_adaptive_resize(_BidirectionalIterator __first, @@ -1161,10 +1147,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2752 | __buffer, __comp); | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from plink.h:21, from binput.cpp:22: @@ -1172,16 +1154,17 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', - inlined from 'void Plink::readSegmentFileMinimal(std::ifstream&)' at input.cpp:1927:25: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/algorithm:61, + from input.cpp:18: +/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2649 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', inlined from 'void Plink::readBinData()' at binput.cpp:97:21: @@ -1256,65 +1239,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5048 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', - inlined from 'void Plink::readHomozygSegmentFile(std::ifstream&)' at input.cpp:2539:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', - inlined from 'void Plink::readSegmentFile(std::ifstream&)' at input.cpp:1862:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from tinput.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -tinput.cpp: In member function 'void Plink::readTransposedData()': -tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 271 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 309 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 591 | if ( c > sample.size()) - | ~~^~~~~~~~~~~~~~~ -tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1636:31: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1687:27: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1747:31: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from tinput.cpp:19: /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -1392,6 +1316,72 @@ | ^~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2401 | __merge_adaptive(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2716 | __merge_sort_with_buffer(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2727:34: +/usr/include/c++/13/bits/stl_algo.h:2706:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2706 | std::__insertion_sort(__first, __first + __chunk_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2709:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2709 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2709:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator >; _RandomAccessIterator2 = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2731:26: +/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2684 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2685 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2687 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2692 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2693 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = Locus*; _RandomAccessIterator2 = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2734:26: +/usr/include/c++/13/bits/stl_algo.h:2684:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2684 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2685 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2687 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2692 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2693 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2692:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1283 | __rotate(_RandomAccessIterator __first, + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2477 | __merge_without_buffer(_BidirectionalIterator __first, @@ -1416,21 +1406,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2521 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readCovListFile()' at input.cpp:1407:31: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readCovListFile()' at input.cpp:1461:27: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool Plink::readCovListFile()' at input.cpp:1521:31: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2785 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -1753,11 +1728,33 @@ | ~~~~~~~~~~~~~~~~~~ 2799 | __comp); | ~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from plink.h:21, + from input.cpp:23: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:69: /usr/include/c++/13/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 263 | _Temporary_buffer<_ForwardIterator, _Tp>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', + inlined from 'void Plink::readSegmentFileMinimal(std::ifstream&)' at input.cpp:1927:25: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': /usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2363 | __rotate_adaptive(_BidirectionalIterator1 __first, @@ -1846,11 +1843,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2752 | __buffer, __comp); | ~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algo.h:69: -/usr/include/c++/13/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': -/usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 263 | _Temporary_buffer<_ForwardIterator, _Tp>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from plink.h:21, from tinput.cpp:23: @@ -1858,218 +1850,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2363 | __rotate_adaptive(_BidirectionalIterator1 __first, - | ^~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', - inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]' at /usr/include/c++/13/bits/stl_algo.h:2394:20: -/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1399 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1400 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive_resize(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2424 | __merge_adaptive_resize(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2432:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2432 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2433 | __len1, __len2, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2460:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2460 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2461 | _Distance(__len1 - __len11), __len22, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2462 | __buffer, __buffer_size); - | ~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2463:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2463 | std::__merge_adaptive_resize(__first, __first_cut, __new_middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2464 | __len11, __len22, - | ~~~~~~~~~~~~~~~~~ - 2465 | __buffer, __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2466:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2466 | std::__merge_adaptive_resize(__new_middle, __second_cut, __last, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2467 | _Distance(__len1 - __len11), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2468 | _Distance(__len2 - __len22), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2469 | __buffer, __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive_resize(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2758 | __stable_sort_adaptive_resize(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2767:45: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2767 | std::__stable_sort_adaptive_resize(__first, __middle, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2768 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2769:45: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2769 | std::__stable_sort_adaptive_resize(__middle, __last, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2770 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2771:39: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2771 | std::__merge_adaptive_resize(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2772 | _Distance(__middle - __first), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2773 | _Distance(__last - __middle), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2774 | __buffer, __buffer_size, - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 2775 | __comp); - | ~~~~~~~ -In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__stable_sort_adaptive_resize(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2778:29: -/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2750 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2751 | __middle - __first, __last - __middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2752 | __buffer, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2477 | __merge_without_buffer(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', - inlined from 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2517:15: -/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1399 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1400 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2518 | std::__merge_without_buffer(__first, __first_cut, __new_middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2519 | __len11, __len22, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2520 | std::__merge_without_buffer(__new_middle, __second_cut, __last, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2521 | __len1 - __len11, __len2 - __len22, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2785 | __inplace_stable_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2790:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2790 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2794:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2794 | std::__inplace_stable_sort(__first, __middle, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2795:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2795 | std::__inplace_stable_sort(__middle, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2796:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2796 | std::__merge_without_buffer(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2797 | __middle - __first, - | ~~~~~~~~~~~~~~~~~~~ - 2798 | __last - __middle, - | ~~~~~~~~~~~~~~~~~~ - 2799 | __comp); - | ~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2084:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: -/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); - | ^~~~~ -In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: -/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2750 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2751 | __middle - __first, __last - __middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2752 | __buffer, __comp); - | ~~~~~~~~~~~~~~~~~ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: -/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5045 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5048 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: -/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); - | ^~~~~ -In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: -/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2750 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2751 | __middle - __first, __last - __middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2752 | __buffer, __comp); - | ~~~~~~~~~~~~~~~~~ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: -/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5045 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5048 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', inlined from 'void Plink::readTransposedData()' at tinput.cpp:132:21: @@ -2144,14 +1924,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5048 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp -input.cpp: In member function 'void Plink::readData()': -input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] - 91 | if ( feof(PED) ) - | ~~~~^~~~~ -input.cpp:60:10: note: 'PED' was declared here - 60 | FILE * PED; - | ^~~ In file included from genome.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2189,6 +1961,16 @@ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] 1189 | int win_end = win_start + par::prune_ld_win; | ^~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', + inlined from 'void Plink::readHomozygSegmentFile(std::ifstream&)' at input.cpp:2539:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', + inlined from 'void Plink::readSegmentFile(std::ifstream&)' at input.cpp:1862:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp In file included from helper.h:24, from helper.cpp:24: @@ -2322,7 +2104,6 @@ helper.cpp:1391:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1391 | for (int j=0; j&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; @@ -2365,6 +2146,21 @@ helper.cpp:2638:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1636:31: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1687:27: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readMultiplePhenoFile()' at input.cpp:1747:31: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ helper.cpp:2671:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2671 | for (int j=1; j::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readCovListFile()' at input.cpp:1407:31: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readCovListFile()' at input.cpp:1461:27: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bool Plink::readCovListFile()' at input.cpp:1521:31: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] 218 | error("Missing an argument for "+s); @@ -2425,16 +2236,266 @@ helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /usr/include/c++/13/bits/stl_algo.h:69: +/usr/include/c++/13/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': +/usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 263 | _Temporary_buffer<_ForwardIterator, _Tp>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2363 | __rotate_adaptive(_BidirectionalIterator1 __first, + | ^~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', + inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]' at /usr/include/c++/13/bits/stl_algo.h:2394:20: +/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1399 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1400 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive_resize(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2424 | __merge_adaptive_resize(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2432:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2432 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2433 | __len1, __len2, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2460:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2460 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2461 | _Distance(__len1 - __len11), __len22, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2462 | __buffer, __buffer_size); + | ~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2463:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2463 | std::__merge_adaptive_resize(__first, __first_cut, __new_middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2464 | __len11, __len22, + | ~~~~~~~~~~~~~~~~~ + 2465 | __buffer, __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2466:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2466 | std::__merge_adaptive_resize(__new_middle, __second_cut, __last, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2467 | _Distance(__len1 - __len11), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2468 | _Distance(__len2 - __len22), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2469 | __buffer, __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive_resize(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2758 | __stable_sort_adaptive_resize(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2758:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2767:45: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2767 | std::__stable_sort_adaptive_resize(__first, __middle, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2768 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2769:45: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2769 | std::__stable_sort_adaptive_resize(__middle, __last, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2770 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2771:39: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2771 | std::__merge_adaptive_resize(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2772 | _Distance(__middle - __first), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2773 | _Distance(__last - __middle), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2774 | __buffer, __buffer_size, + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 2775 | __comp); + | ~~~~~~~ +In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__stable_sort_adaptive_resize(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2778:29: +/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2750 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2751 | __middle - __first, __last - __middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2752 | __buffer, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2477 | __merge_without_buffer(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', + inlined from 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:2517:15: +/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1399 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1400 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2518 | std::__merge_without_buffer(__first, __first_cut, __new_middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2519 | __len11, __len22, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2520 | std::__merge_without_buffer(__new_middle, __second_cut, __last, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2521 | __len1 - __len11, __len2 - __len22, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2785 | __inplace_stable_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2790:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2790 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2794:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2794 | std::__inplace_stable_sort(__first, __middle, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2795:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2795 | std::__inplace_stable_sort(__middle, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2796:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2796 | std::__merge_without_buffer(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2797 | __middle - __first, + | ~~~~~~~~~~~~~~~~~~~ + 2798 | __last - __middle, + | ~~~~~~~~~~~~~~~~~~ + 2799 | __comp); + | ~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2084:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: +/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); + | ^~~~~ +In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: +/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2750 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2751 | __middle - __first, __last - __middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2752 | __buffer, __comp); + | ~~~~~~~~~~~~~~~~~ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2112:14: +/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5045 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5048 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: +/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); + | ^~~~~ +In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: +/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2750 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2751 | __middle - __first, __last - __middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2752 | __buffer, __comp); + | ~~~~~~~~~~~~~~~~~ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)' at input.cpp:2134:14: +/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5045 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5048 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp +input.cpp: In member function 'void Plink::readData()': +input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] + 91 | if ( feof(PED) ) + | ~~~~^~~~~ +input.cpp:60:10: note: 'PED' was declared here + 60 | FILE * PED; + | ^~~ In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from filters.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] 458 | int m,l,iter,i,k; | ^ +filters.cpp: In member function 'void Plink::filterSNPs()': +filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 95 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 123 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 132 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 155 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 163 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 198 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 273 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 591 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1477 | for (int c = 0 ; c < keep.size(); c++) @@ -2463,7 +2539,31 @@ stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1531 | for (int i = 0; i < v.size(); i++) | ~~^~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp +filters.cpp:739:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 739 | for ( int l = 0 ; l < locus.size() ; l++ ) + | ~~^~~~~~~~~~~~~~ +filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 762 | for ( int i = 0 ; i < sample.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ +filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1078 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1091 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1165 | for ( int i=0; i::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > svd_inverse(std::vector >&, bool&)' at stats.cpp:856:16: @@ -2498,83 +2599,20 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from filters.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -filters.cpp: In member function 'void Plink::filterSNPs()': -filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 95 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 123 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 132 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 155 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 163 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 198 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 273 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 591 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 739 | for ( int l = 0 ; l < locus.size() ; l++ ) - | ~~^~~~~~~~~~~~~~ -filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 762 | for ( int i = 0 ; i < sample.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1078 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1091 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1165 | for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp In file included from /usr/include/c++/13/vector:72, from helper.h:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2639,60 +2677,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcSinglePoint()' at multi.cpp:35:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcSinglePoint()' at multi.cpp:41:16: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:78:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:90:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:103:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:116:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:126:21: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:135:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:144:16: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from helper.h:24, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -2823,6 +2807,59 @@ cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcSinglePoint()' at multi.cpp:35:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcSinglePoint()' at multi.cpp:41:16: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:78:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:90:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:103:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:116:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:126:21: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:135:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void Plink::preCalcMultiPoint()' at multi.cpp:144:16: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from cluster.cpp:19: @@ -2835,6 +2872,24 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from mds.cpp:21: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +mds.cpp: In member function 'void Plink::generateMDS()': +mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] + 191 | for (int i2=0; i2::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -2843,7 +2898,6 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from /usr/include/c++/13/vector:72, from plink.h:21, from cluster.cpp:22: @@ -2855,40 +2909,25 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/set:62, + from plink.h:22, + from mds.cpp:20: +/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63, + from plink.h:23: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = double; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = double; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::generateMDS()' at mds.cpp:261:16: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp -In file included from mds.cpp:21: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -mds.cpp: In member function 'void Plink::generateMDS()': -mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] - 191 | for (int i2=0; i2::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] - 242 | bool flag = svd(D,eigenvalue,eigenvector); - | ^~~~ -In file included from output.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::displayGenomePV()': -output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 86 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 89 | for (int k=0; k::iterator loc1 = locus.begin()+m1; - | ^~~~ -output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] - 403 | vector::iterator loc2 = locus.begin()+m2; - | ^~~~ -output.cpp: In member function 'void Plink::extractExcludeSet(bool)': -output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 520 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 526 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 553 | for (int l=0; l::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Plink::buildCluster()' at cluster.cpp:259:14: @@ -2985,6 +3003,57 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from output.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from informative.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::displayGenomePV()': +output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 86 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 89 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 80 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 102 | if ( col_length != tokens.size() ) + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 105 | for (int i=0;i::iterator loc1 = locus.begin()+m1; + | ^~~~ +output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] + 403 | vector::iterator loc2 = locus.begin()+m2; + | ^~~~ +output.cpp: In member function 'void Plink::extractExcludeSet(bool)': +output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 520 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 526 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 553 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63, - from plink.h:23: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = double; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = double; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::generateMDS()' at mds.cpp:261:16: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp -In file included from informative.cpp:18: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -informative.cpp: In member function 'int Plink::readInformative()': -informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 80 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 102 | if ( col_length != tokens.size() ) - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 105 | for (int i=0;i >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp In file included from /usr/include/c++/13/set:62, from plink.h:22: /usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = Pair; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::groupGenome()' at cluster.cpp:1613:17: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63, from plink.h:23: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = Pair; _Tp = Z; _Compare = std::less; _Alloc = std::allocator >]', @@ -3091,15 +3110,6 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_indivReport()': -output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 69 | << setw(6) << genotype(*this,i1,l) << "\n"; - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:46:7: note: 'i1' was declared here - 46 | int i1; - | ^~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp In file included from helper.h:24, from assoc.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3131,6 +3141,25 @@ assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp +output.cpp: In member function 'void Plink::display_pairList()': +output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] + 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:7: note: 'i1' was declared here + 116 | int i1, i2; + | ^~ +output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] + 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:11: note: 'i2' was declared here + 116 | int i1, i2; + | ^~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::groupGenome()' at cluster.cpp:1613:17: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3152,7 +3181,13 @@ epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] 701 | int c=0; | ^ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp +output.cpp: In member function 'void Plink::display_indivReport()': +output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] + 69 | << setw(6) << genotype(*this,i1,l) << "\n"; + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:46:7: note: 'i1' was declared here + 46 | int i1; + | ^~ In file included from /usr/include/c++/13/vector:72, from plink.h:21, from assoc.cpp:21: @@ -3162,7 +3197,7 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'std::vector Plink::testMiss(Perm&, bool)' at assoc.cpp:2235:19: @@ -3175,6 +3210,13 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': +assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] + 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) + | ^~ +assoc.cpp:1019:14: note: 'pvalue' was declared here + 1019 | double pvalue; + | ^~~~~~ In file included from prephap.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3211,13 +3253,7 @@ prephap.cpp:560:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 560 | for (int i=0; i Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': -assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] - 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) - | ^~ -assoc.cpp:1019:14: note: 'pvalue' was declared here - 1019 | double pvalue; - | ^~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp In file included from /usr/include/c++/13/iostream:41, from assoc.cpp:14: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', @@ -3362,63 +3398,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from phase.cpp:19: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::enumerateHaplotypes(std::vector&)' at phase.cpp:466:19: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::enumerateHaplotypes(std::vector&)' at phase.cpp:467:21: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::prunePhase(int)' at phase.cpp:1833:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1078:35: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1091:39: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1225:16: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1226:18: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1506:28: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1588:37: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -3429,6 +3409,12 @@ trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 91 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from phase.cpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 258 | for (int k=0; kkid.size(); k++) @@ -3458,6 +3444,10 @@ trio.cpp:504:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 504 | for (int c=0; c::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ trio.cpp:871:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 871 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::enumerateHaplotypes(std::vector&)' at phase.cpp:466:19: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::enumerateHaplotypes(std::vector&)' at phase.cpp:467:21: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::prunePhase(int)' at phase.cpp:1833:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3529,6 +3535,7 @@ tdt.cpp:415:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 415 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 522 | for (int f=0; f::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:301:17: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:302:19: + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1078:35: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1091:39: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:306:25: + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1225:16: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:307:26: + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1226:18: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:374:20: + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1506:28: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::performAlternEM()' at phase.cpp:1588:37: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ @@ -3573,14 +3585,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp -tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': -tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] - 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; - | ~~~^~~~~~~~~~~~~~~~~ -tdt.cpp:460:10: note: 'zt' was declared here - 460 | double zt; - | ^~ In file included from perm.h:17, from sharing.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -3591,14 +3595,45 @@ sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 102 | for (int l=0; l Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': +tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] + 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; + | ~~~^~~~~~~~~~~~~~~~~ +tdt.cpp:460:10: note: 'zt' was declared here + 460 | double zt; + | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:301:17: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:302:19: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:306:25: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:307:26: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)' at phase.cpp:374:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Plink::perm_testTDT(Perm&)' at tdt.cpp:186:15: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp In file included from genepi.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3649,6 +3684,20 @@ genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from genepi.cpp:19: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3759,18 +3808,6 @@ sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from genepi.cpp:20: @@ -3807,6 +3844,30 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from perm.h:17, + from perm.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +perm.cpp: In member function 'void Perm::permuteInCluster()': +perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 144 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 145 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] + 187 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 199 | for(int i=0; i&, std::vector&)': +perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 273 | for (int j=0;j< P.pS->snpset[l].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)' at genepi.cpp:1145:17: @@ -3839,6 +3900,13 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from perm.cpp:15: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -3847,6 +3915,54 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Pair2; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'bool Perm::update(std::vector&, std::vector&)' at perm.cpp:370:8: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'bool Perm::update(std::vector&, std::vector&)' at perm.cpp:370:8: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; @@ -3895,19 +4011,51 @@ 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, + from options.h:18: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Pair2&}; _Tp = Pair2; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Pair2; _Alloc = std::allocator]', + inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:192:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:195:7: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:195:7: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, from plink.h:21, from sets.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'vector_t Set::profileTestScore()' at sets.cpp:788:24: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Set::profileTestSNPInformation(int, double)' at sets.cpp:684:36: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3933,129 +4081,17 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from perm.h:17, - from perm.cpp:17: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -perm.cpp: In member function 'void Perm::permuteInCluster()': -perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 144 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 145 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] - 187 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 199 | for(int i=0; i&, std::vector&)': -perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 273 | for (int j=0;j< P.pS->snpset[l].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from perm.cpp:15: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Pair2; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'bool Perm::update(std::vector&, std::vector&)' at perm.cpp:370:8: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'bool Perm::update(std::vector&, std::vector&)' at perm.cpp:370:8: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from options.h:18: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Pair2&}; _Tp = Pair2; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 747 | for (int i=0; i::push_back(const value_type&) [with _Tp = Pair2; _Alloc = std::allocator]', - inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:192:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:195:7: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void Perm::setOriginalRanking(vector_t&)' at perm.cpp:195:7: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1249 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -4122,6 +4157,7 @@ merge.cpp:842:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 842 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -4134,12 +4170,6 @@ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 173 | for (int s=0; s::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from merge.cpp:19: /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -4152,12 +4182,6 @@ /usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)' at hotel.cpp:458:21: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2401 | __merge_adaptive(_BidirectionalIterator __first, @@ -4224,6 +4248,12 @@ | ^~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1283:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from hotel.cpp:18: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2477:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2477 | __merge_without_buffer(_BidirectionalIterator __first, @@ -4248,6 +4278,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2521 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)' at hotel.cpp:458:21: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2785 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -4570,7 +4606,6 @@ | ~~~~~~~~~~~~~~~~~~ 2799 | __comp); | ~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp In file included from helper.h:24, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': @@ -4596,6 +4631,8 @@ /usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 263 | _Temporary_buffer<_ForwardIterator, _Tp>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from multiple.cpp:18: @@ -4608,6 +4645,19 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2363 | __rotate_adaptive(_BidirectionalIterator1 __first, + | ^~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', + inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]' at /usr/include/c++/13/bits/stl_algo.h:2394:20: +/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1399 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1400 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -4622,19 +4672,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2363 | __rotate_adaptive(_BidirectionalIterator1 __first, - | ^~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2363:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function '_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]', - inlined from '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]' at /usr/include/c++/13/bits/stl_algo.h:2394:20: -/usr/include/c++/13/bits/stl_algo.h:1399:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1399 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1400 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive_resize(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2424:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2424 | __merge_adaptive_resize(_BidirectionalIterator __first, @@ -4742,11 +4779,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5048 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from haploCC.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from plink.h:21, from merge.cpp:21: @@ -4811,6 +4843,37 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from haploTDT.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from haploCC.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', + inlined from 'void Plink::mergeData()' at merge.cpp:304:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', + inlined from 'void Plink::mergeData()' at merge.cpp:330:14: +/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, + | ^ +In file included from haploTDT.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >]', + inlined from 'void Plink::mergeData()' at merge.cpp:354:14: +/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, + | ^ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -4845,25 +4908,9 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', - inlined from 'void Plink::mergeData()' at merge.cpp:304:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', - inlined from 'void Plink::mergeData()' at merge.cpp:330:14: -/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, - | ^ -In function 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', - inlined from 'void Plink::mergeData()' at merge.cpp:354:14: -/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, - | ^ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp In file included from /usr/include/c++/13/vector:72, - from haploCC.cpp:20: + from haploTDT.cpp:20: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4872,52 +4919,42 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::haplotypicWeightedCC()' at haploCC.cpp:315:21: + inlined from 'void HaploPhase::haplotypicWeightedTDT()' at haploTDT.cpp:177:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void HaploPhase::haplotypicWeightedCC()' at haploCC.cpp:319:21: + inlined from 'void HaploPhase::haplotypicWeightedTDT()' at haploTDT.cpp:181:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp -In file included from haploTDT.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploTDT.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from poo.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::haplotypicWeightedTDT()' at haploTDT.cpp:177:21: + inlined from 'void HaploPhase::haplotypicWeightedCC()' at haploCC.cpp:315:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void HaploPhase::haplotypicWeightedTDT()' at haploTDT.cpp:181:21: + inlined from 'void HaploPhase::haplotypicWeightedCC()' at haploCC.cpp:319:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from poo.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 93 | for (int f=0; f::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::perm_testTDT_POO(Perm&)' at poo.cpp:59:15: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) @@ -4991,6 +5020,12 @@ qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 97 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::perm_testTDT_POO(Perm&)' at poo.cpp:59:15: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 267 | for (int i=0; i < family.size(); i++) @@ -5011,7 +5046,16 @@ qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] 639 | int tc = 0; | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp +In file included from /usr/include/c++/13/vector:72, + from plink.h:21, + from qfam.cpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -5026,18 +5070,16 @@ linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; | ^~~~ -In file included from /usr/include/c++/13/vector:72, - from plink.h:21, - from qfam.cpp:19: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from bmerge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from parse.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] 90 | long int inc; @@ -5081,6 +5123,7 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:96:5: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] 96 | if (irow != icol) { @@ -5094,7 +5137,17 @@ linear.cpp:75:14: note: 'irow' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp +In file included from /usr/include/c++/13/algorithm:61, + from bmerge.cpp:19: +/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2649 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from linear.h:17, from linear.cpp:18: @@ -5108,6 +5161,12 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2401 | __merge_adaptive(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void LinearModel::fitLM()' at linear.cpp:277:13: /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -5118,6 +5177,11 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from mishap.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -5132,34 +5196,29 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/algorithm:61, - from bmerge.cpp:19: -/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2649 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2649:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2401 | __merge_adaptive(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:2401:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from parse.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from mishap.cpp:20: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +mishap.cpp: In member function 'void Plink::performMisHapTests()': +mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2716:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2716 | __merge_sort_with_buffer(_RandomAccessIterator __first, @@ -5239,6 +5298,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2521 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2785:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2785 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -5561,29 +5621,6 @@ | ~~~~~~~~~~~~~~~~~~ 2799 | __comp); | ~~~~~~~ -In file included from mishap.cpp:17: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from mishap.cpp:20: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:69: /usr/include/c++/13/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/13/bits/stl_tempbuf.h:263:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -5716,53 +5753,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:301:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:354:14: -/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, - | ^ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: -/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); - | ^~~~~ -In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: -/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2750 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2751 | __middle - __first, __last - __middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2752 | __buffer, __comp); - | ~~~~~~~~~~~~~~~~~ -In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: -/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5045 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5048 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': @@ -5809,6 +5799,92 @@ legacy.cpp:480:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | for (int i=0; i::push_back(const value_type&) [with _Tp = Locus; _Alloc = std::allocator]', + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:301:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:354:14: +/usr/include/c++/13/bits/stl_algo.h:5083:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5083 | _GLIBCXX_STD_A::__stable_sort(__first, __last, + | ^ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: +/usr/include/c++/13/bits/stl_algo.h:5038:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5038 | _TmpBuf __buf(__first, (__last - __first + 1) / 2); + | ^~~~~ +In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:5041:29, + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: +/usr/include/c++/13/bits/stl_algo.h:2747:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2747 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2748:36: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2748 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:2750:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2750 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2751 | __middle - __first, __last - __middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2752 | __buffer, __comp); + | ~~~~~~~~~~~~~~~~~ +In function 'void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:5083:36, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:370:14: +/usr/include/c++/13/bits/stl_algo.h:5045:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5045 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:5047:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5047 | std::__stable_sort_adaptive_resize(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5048 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from plink.h:21, + from legacy.cpp:21: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': +legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] + 203 | << start - last - 1 << " "; + | ~~~~~~^~~~~~ +legacy.cpp:35:7: note: 'last' was declared here + 35 | int last; + | ^~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', + inlined from 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)' at legacy.cpp:177:25: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::preCalcRegression_PIHAT()' at legacy.cpp:716:24: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::preCalcRegression_PIHAT()' at legacy.cpp:722:24: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::calcRegression(int)' at legacy.cpp:549:23: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -5856,46 +5932,7 @@ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; -In file included from /usr/include/c++/13/vector:72, - from plink.h:21, - from legacy.cpp:21: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': -legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] - 203 | << start - last - 1 << " "; - | ~~~~~~^~~~~~ -legacy.cpp:35:7: note: 'last' was declared here - 35 | int last; - | ^~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', - inlined from 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)' at legacy.cpp:177:25: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::preCalcRegression_PIHAT()' at legacy.cpp:716:24: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::preCalcRegression_PIHAT()' at legacy.cpp:722:24: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::calcRegression(int)' at legacy.cpp:549:23: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -5974,6 +6011,65 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ +In file included from model.cpp:15: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from model.cpp:17: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&)': +model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 132 | if ( include.size() != P->n ) + | ~~~~~~~~~~~~~~~^~~~~~~ +model.cpp: In member function 'void Model::buildDesignMatrix()': +model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 354 | for (int i=0; i< par::parameter_list.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 367 | for ( int i = 0 ; i < X.size() ; i++) + | ~~^~~~~~~~~~ +model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'bool Model::checkVIF()': +model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] + 613 | double maxVIF = 0; + | ^~~~~~ +model.cpp: In member function 'double Model::buildQFAM(Individual*)': +model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] + 849 | error("Internal problem with QFAM model specification"); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from model.h:17, + from model.cpp:14: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double Model::linearHypothesis(matrix_t&, vector_t&)' at model.cpp:496:15: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double Model::linearHypothesis(matrix_t&, vector_t&)' at model.cpp:528:14: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Model::buildDesignMatrix()' at model.cpp:379:15: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from homozyg.cpp:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': @@ -5986,11 +6082,7 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', - inlined from 'void Plink::findHomoRuns(Individual*, std::ofstream&)' at homozyg.cpp:1918:25: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp In file included from /usr/include/c++/13/vector:72, from plink.h:21, from segment.cpp:19: @@ -6004,6 +6096,11 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', + inlined from 'void Plink::findHomoRuns(Individual*, std::ofstream&)' at homozyg.cpp:1918:25: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -6021,6 +6118,20 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from logistic.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': +logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = indivPair; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -6083,76 +6194,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp -In file included from model.cpp:15: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from model.cpp:17: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i&)': -model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 132 | if ( include.size() != P->n ) - | ~~~~~~~~~~~~~~~^~~~~~~ -model.cpp: In member function 'void Model::buildDesignMatrix()': -model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 354 | for (int i=0; i< par::parameter_list.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 367 | for ( int i = 0 ; i < X.size() ; i++) - | ~~^~~~~~~~~~ -model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp -model.cpp: In member function 'bool Model::checkVIF()': -model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] - 613 | double maxVIF = 0; - | ^~~~~~ -model.cpp: In member function 'double Model::buildQFAM(Individual*)': -model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] - 849 | error("Internal problem with QFAM model specification"); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from logistic.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': -logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double Model::linearHypothesis(matrix_t&, vector_t&)' at model.cpp:496:15: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double Model::linearHypothesis(matrix_t&, vector_t&)' at model.cpp:528:14: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from logistic.h:17, from logistic.cpp:18: @@ -6171,11 +6212,6 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Model::buildDesignMatrix()' at model.cpp:379:15: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': @@ -6238,6 +6274,7 @@ glm.cpp:423:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 423 | for (int c=0; c::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': -glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] - 610 | double pvalue = chiprobP(chisq,df); - | ~~~~~~~~^~~~~~~~~~ -glm.cpp:556:15: note: 'df' was declared here - 556 | int df; - | ^~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:566:16: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:579:16: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:595:16: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp In file included from helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -6304,6 +6316,31 @@ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ +glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': +glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] + 610 | double pvalue = chiprobP(chisq,df); + | ~~~~~~~~^~~~~~~~~~ +glm.cpp:556:15: note: 'df' was declared here + 556 | int df; + | ^~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:566:16: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:579:16: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'vector_t Plink::glmAssoc(bool, Perm&)' at glm.cpp:595:16: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6343,7 +6380,6 @@ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp In file included from /usr/include/c++/13/vector:72, from plink.h:21, from elf.cpp:18: @@ -6355,10 +6391,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'bool RCount::addSNP(int)': -elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] - 374 | double wt; - | ^~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': @@ -6414,6 +6446,10 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'bool RCount::addSNP(int)': +elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] + 374 | double wt; + | ^~ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1538 | prterr(6, "LDKEY is too small for this problem.\n" @@ -6455,6 +6491,7 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'RCount::RCount(Plink*, std::map*)' at elf.cpp:39:16, inlined from 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)' at elf.cpp:700:25, @@ -6474,6 +6511,33 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from linput.cpp:25: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +linput.cpp: In member function 'void Plink::readDataLongFormat()': +linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 68 | for (int l=0; l< locus.size(); l++) + | ~^~~~~~~~~~~~~~ +linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 128 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 136 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 146 | for (int l=0; l< locus.size(); l++) + | ~^~~~~~~~~~~~~~ +linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 164 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 209 | for (int i=0; i::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -6498,6 +6562,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1159:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1159 | ++(*p_cnt); @@ -6511,35 +6576,6 @@ elf.cpp:1112:13: note: 'p_gcnt' was declared here 1112 | int * p_gcnt; | ^~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp -In file included from linput.cpp:25: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -linput.cpp: In member function 'void Plink::readDataLongFormat()': -linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 68 | for (int l=0; l< locus.size(); l++) - | ~^~~~~~~~~~~~~~ -linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 128 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 136 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 146 | for (int l=0; l< locus.size(); l++) - | ~^~~~~~~~~~~~~~ -linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 164 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 209 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 289 | for (int i=25; i::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/set:62, - from proxy.cpp:17: -/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from haploQTL.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -6653,20 +6677,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:370:14, - inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:392:16, - inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:385:24, - inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1087:23, - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: -/usr/include/c++/13/bits/stl_bvector.h:229:11: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] - 229 | __n = __n % int(_S_word_bit); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -proxy.cpp: In member function 'void Plink::performProxyTests(int)': -proxy.cpp:422:7: note: 'ref' was declared here - 422 | int ref; - | ^~~ haploQTL.cpp: In member function 'void HaploPhase::haplotypicQTL(std::map&, int, bool)': haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int z = 0 ; z < hap1[i].size(); z++) @@ -6674,39 +6684,20 @@ haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63, - from plink.h:23, - from options.h:19: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:371:23: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:973:27: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:974:29: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:1519:24: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:1520:26: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from options.h:18: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp +In file included from /usr/include/c++/13/set:62, + from proxy.cpp:17: +/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6807,7 +6798,6 @@ haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6827,6 +6817,20 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:370:14, + inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:392:16, + inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:385:24, + inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1087:23, + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: +/usr/include/c++/13/bits/stl_bvector.h:229:11: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] + 229 | __n = __n % int(_S_word_bit); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +proxy.cpp: In member function 'void Plink::performProxyTests(int)': +proxy.cpp:422:7: note: 'ref' was declared here + 422 | int ref; + | ^~~ haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) @@ -6871,23 +6875,38 @@ haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63, + from plink.h:23, + from options.h:19: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:371:23: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::enumerateAllPhases()' at haplohelper.cpp:254:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::enumerateAllPhases()' at haplohelper.cpp:270:30: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:973:27: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:974:29: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:1519:24: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:1520:26: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from haplowindow.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -6910,7 +6929,23 @@ 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp +In file included from /usr/include/c++/13/vector:72, + from haplohelper.cpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::enumerateAllPhases()' at haplohelper.cpp:254:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::enumerateAllPhases()' at haplohelper.cpp:270:30: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from genogroup.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6930,11 +6965,13 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp In file included from nonfounderphasing.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6960,34 +6997,7 @@ nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp -In file included from /usr/include/c++/13/vector:72, - from nonfounderphasing.cpp:19: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:62, - from nonfounderphasing.cpp:20: -/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = FamilyTransmissions; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = FamilyTransmissions; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = FamilyTransmissions; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void HaploPhase::phaseAndScoreNonfounder(int)' at nonfounderphasing.cpp:563:20: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void HaploPhase::phaseAndScoreNonfounder(int)' at nonfounderphasing.cpp:651:23: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: @@ -7038,7 +7048,18 @@ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp +In file included from /usr/include/c++/13/vector:72, + from nonfounderphasing.cpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:62, + from nonfounderphasing.cpp:20: +/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = FamilyTransmissions; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7083,6 +7104,22 @@ genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 358 | for (int z2=0; z2::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = FamilyTransmissions; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = FamilyTransmissions; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void HaploPhase::phaseAndScoreNonfounder(int)' at nonfounderphasing.cpp:563:20: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void HaploPhase::phaseAndScoreNonfounder(int)' at nonfounderphasing.cpp:651:23: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp In file included from /usr/include/c++/13/vector:72, from genoerr.cpp:19: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -7100,17 +7137,58 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/bits/stl_algo.h:61: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ResultTrio; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)' at genoerr.cpp:192:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algo.h:61: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ResultTrio; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from em.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from em.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 89 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 97 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 106 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 128 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 132 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 162 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 166 | for (int z=0; z::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ResultTrio&}; _Tp = ResultTrio; _Alloc = std::allocator]': @@ -7127,9 +7205,10 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp /usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -7173,12 +7252,12 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from em.cpp:24: +In file included from impute.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from em.cpp:27: +In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 89 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 97 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 106 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 128 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 132 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 162 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 166 | for (int z=0; z::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void clump_LD::clump()' at clumpld.cpp:546:25: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void clump_LD::clump()' at clumpld.cpp:633:25: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp -In file included from impute.cpp:24: +In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from impute.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ -In file included from /usr/include/c++/13/map:62, - from impute.cpp:20: -/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void HaploPhase::updateForImputation()' at impute.cpp:130:21: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp -In file included from metaem.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7311,6 +7315,38 @@ metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 239 | while (h::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void clump_LD::clump()' at clumpld.cpp:546:25: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void clump_LD::clump()' at clumpld.cpp:633:25: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int2; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void HaploPhase::updateForImputation()' at impute.cpp:130:21: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp In file included from profile.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7355,59 +7391,8 @@ profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 667 | for (int l=0; l::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double2&}; _Tp = double2; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)' at profile.cpp:440:17: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp -In file included from /usr/include/c++/13/map:62, - from profile.cpp:20: -/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::scoreIndividuals()' at profile.cpp:76:19: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double2; _Alloc = std::allocator]', - inlined from 'void Plink::scoreIndividuals()' at profile.cpp:91:21: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::scoreIndividuals()' at profile.cpp:192:21: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::scoreIndividuals()' at profile.cpp:198:21: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp In file included from helper.h:24, from nlist.h:21, from nlist.cpp:17: @@ -7446,20 +7431,22 @@ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp -In file included from helper.h:24, - from simul.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from profile.cpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double2&}; _Tp = double2; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7484,39 +7471,24 @@ whap.cpp:511:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -simul.cpp: In member function 'void Plink::simulateSNPs()': -simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 635 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ -simul.cpp:679:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 679 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ -simul.cpp: In member function 'void Plink::simulateSNPs_QT()': -simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1146 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1211 | for (int s=0; s::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)' at profile.cpp:440:17: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 962 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:62, + from profile.cpp:20: +/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp +In file included from /usr/include/c++/13/map:63: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::scoreIndividuals()' at profile.cpp:76:19: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double2; _Alloc = std::allocator]', + inlined from 'void Plink::scoreIndividuals()' at profile.cpp:91:21: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::scoreIndividuals()' at profile.cpp:192:21: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::scoreIndividuals()' at profile.cpp:198:21: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from simul.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': +simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] + 172 | double gh_11_12 = h11*h12; + | ^~~~~~~~ +simul.cpp: In member function 'void Plink::simulateSNPs()': +simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 635 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 679 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1146 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1211 | for (int s=0; s::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from /usr/include/c++/13/vector:72, from plink.h:21, from simul.cpp:15: @@ -7579,58 +7623,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SimParametersQT&}; _Tp = SimParametersQT; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:72, - from whap.h:18, - from whap.cpp:19: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SimParameters; _Alloc = std::allocator]', - inlined from 'void Plink::simulateSNPs()' at simul.cpp:619:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::simulateSNPs()' at simul.cpp:857:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::simulateSNPs()' at simul.cpp:863:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SimParametersQT; _Alloc = std::allocator]', - inlined from 'void Plink::simulateSNPs_QT()' at simul.cpp:1130:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::simulateSNPs_QT()' at simul.cpp:1363:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:304:31: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:408:30: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:413:30: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24, from gvar.cpp:15: options.h: In member function 'void OptionSet::display()': @@ -7674,13 +7666,89 @@ gvar.cpp:556:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 556 | for (int i=0; i::push_back(const value_type&) [with _Tp = SimParameters; _Alloc = std::allocator]', + inlined from 'void Plink::simulateSNPs()' at simul.cpp:619:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::simulateSNPs()' at simul.cpp:857:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::simulateSNPs()' at simul.cpp:863:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:304:31: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:408:30: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)' at whap.cpp:413:30: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SimParametersQT; _Alloc = std::allocator]', + inlined from 'void Plink::simulateSNPs_QT()' at simul.cpp:1130:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::simulateSNPs_QT()' at simul.cpp:1363:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from helper.h:24, from cnv.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from gvar.h:17, + from gvar.cpp:14: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1080:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1076:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1071:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1072:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; @@ -7745,7 +7813,6 @@ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': @@ -7780,37 +7847,13 @@ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ -In file included from /usr/include/c++/13/vector:72, - from gvar.h:17, - from gvar.cpp:14: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1080:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1076:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1071:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'Model* analyseModel(Plink*, Variant*, int, bool, bool)' at gvar.cpp:1072:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp +In file included from helper.h:24, + from flip.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from cnv.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': @@ -7821,8 +7864,17 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp +In file included from helper.h:24, + from qualscores.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': +qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] + 122 | long int nfound = 0; + | ^~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Segment; _Alloc = std::allocator]', inlined from 'void Plink::readCNVList()' at cnv.cpp:599:21: @@ -7839,30 +7891,14 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from flip.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from qualscores.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': -qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] - 122 | long int nfound = 0; - | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from /usr/include/c++/13/vector:72, from cnvqt.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -7912,21 +7948,11 @@ | ~~^~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp -In file included from idhelp.cpp:18: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from idhelp.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 80 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from setscreen.cpp:18: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SortedResult; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from idhelp.cpp:18: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) @@ -7947,6 +8004,12 @@ idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 63 | for (int i=0; i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SortedResult&}; _Tp = SortedResult; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'bool IDHelper::matchIndividual(IDGroup*, std::map >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) @@ -7964,7 +8027,6 @@ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 296 | for ( int i = 0 ; i < mask.size() ; i++) | ~~^~~~~~~~~~~~~ @@ -8154,6 +8216,32 @@ idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SortedResult; _Alloc = std::allocator]', + inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:205:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:227:11: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:227:11: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) @@ -8206,66 +8294,13 @@ idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from setscreen.cpp:18: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SortedResult; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from options.h:18: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SortedResult&}; _Tp = SortedResult; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SortedResult; _Alloc = std::allocator]', - inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:205:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:227:11: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void Plink::setAssocSummary()' at setscreen.cpp:227:11: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -8277,25 +8312,7 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -lookup2.cpp: In member function 'void Plink::lookup2()': -lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 163 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 203 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 280 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 325 | for (int t = 0 ; t < tokens.size() ; t++) - | ~~^~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from /usr/include/c++/13/vector:72, from whap.h:18, from hapglm.cpp:19: @@ -8318,6 +8335,25 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from helper.h:24, + from lookup2.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +lookup2.cpp: In member function 'void Plink::lookup2()': +lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 163 | for (int i = 0 ; i < ids.size(); i++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 203 | for (int i = 0 ; i < ids.size(); i++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 280 | for (int i = 0 ; i < ids.size(); i++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 325 | for (int t = 0 ; t < tokens.size() ; t++) + | ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -8359,12 +8395,6 @@ 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp -In file included from helper.h:24, - from zed.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ blox.cpp:510:10: warning: 'pA1' may be used uninitialized [-Wmaybe-uninitialized] 510 | double D = pA1 - (pA*p1); | ^ @@ -8396,6 +8426,12 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from zed.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63, from plink.h:23: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int2; _Tp = DPrime; _Compare = std::less; _Alloc = std::allocator >]', @@ -8422,11 +8458,6 @@ dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ -In file included from annot.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 513 | for (int i=0; i >::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) +dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 989 | for (int q=0; qgetStatistic() : 0; + | ^~~~~~~~~ +dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1252 | if ( o->second != dosageFilename_all.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1310 | if ( ++qq == qthresh.size() ) + | ~~~~~^~~~~~~~~~~~~~~~~ +dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] + 190 | int geno_field = a2_field + skip2 + 1; + | ^~~~~~~~~~ +In file included from annot.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int j=1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 989 | for (int q=0; q >::size_type' {aka 'unsigned int'} [-Wsign-compare] 149 | for (int i=0; igetStatistic() : 0; - | ^~~~~~~~~ annot.cpp:250:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 250 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ @@ -8466,18 +8511,9 @@ annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 260 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1252 | if ( o->second != dosageFilename_all.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 275 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1310 | if ( ++qq == qthresh.size() ) - | ~~~~~^~~~~~~~~~~~~~~~~ -dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] - 190 | int geno_field = a2_field + skip2 + 1; - | ^~~~~~~~~~ annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] 300 | bool include = false; | ^~~~~~~ @@ -8646,6 +8682,20 @@ r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ +In file included from /usr/include/c++/13/vector:72, + from stats.h:19, + from metaanal.cpp:20: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/set:62, + from plink.h:22, + from stats.h:22: +/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -8676,26 +8726,41 @@ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ -In file included from /usr/include/c++/13/vector:72, - from stats.h:19, - from metaanal.cpp:20: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/set:62, - from plink.h:22, - from stats.h:22: -/usr/include/c++/13/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.h:42, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ +In file included from /usr/include/c++/13/map:63, + from plink.h:23: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:418:16: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:425:24: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:525:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:526:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 203 | { name=""; fix_content(); } @@ -8726,35 +8791,6 @@ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 567 | if (host) free(host); host=0; | ^~~~ -In file included from /usr/include/c++/13/map:63, - from plink.h:23: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:418:16: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = SInfo; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:425:24: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:525:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Plink::metaAnalysis()' at metaanal.cpp:526:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DWITH_R_PLUGINS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' @@ -8800,12 +8836,14 @@ 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/2336/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2336/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/25552 and its subdirectories -I: Current time: Tue May 21 16:14:47 -12 2024 -I: pbuilder-time-stamp: 1716351287 +I: removing directory /srv/workspace/pbuilder/2336 and its subdirectories +I: Current time: Wed May 22 18:46:46 +14 2024 +I: pbuilder-time-stamp: 1716353206