Diff of the two buildlogs: -- --- b1/build.log 2025-01-25 16:15:11.072870117 +0000 +++ b2/build.log 2025-01-25 16:19:00.470520346 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 27 10:36:19 -12 2026 -I: pbuilder-time-stamp: 1772231779 +I: Current time: Sun Jan 26 06:15:13 +14 2025 +I: pbuilder-time-stamp: 1737821713 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,54 +28,86 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/64070/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27197/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 25 16:15 /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/27197/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27197/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='2f4cc83e771946a88ca62bb4b1cd3522' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='64070' - PS1='# ' - PS2='> ' + INVOCATION_ID=47b660b6f13f499498d8895c5131674b + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27197 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.ND6XjfLg/pbuilderrc_m5Op --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ND6XjfLg/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ND6XjfLg/pbuilderrc_s7tH --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ND6XjfLg/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/64070/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/27197/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 21.7 MB in 0s (134 MB/s) +Fetched 21.7 MB in 1s (40.2 MB/s) Preconfiguring packages ... 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 ... 19818 files and directories currently installed.) @@ -283,7 +315,11 @@ 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/27197/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/27197/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 @@ -295,7 +331,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j22 clean + make -j10 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' @@ -310,7 +346,7 @@ 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 - make -j22 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 + make -j10 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp @@ -322,85 +358,16 @@ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp In file included from locus.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 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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from cluster.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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ -In file included from genome.cpp:24: +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 prephap.cpp:24: +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++) | ~~^~~~~~~~~~~~~~~~~~ -multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': -multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 295 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 304 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 357 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -multi.cpp:372:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 372 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from filters.cpp:24: +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] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -471,19 +426,81 @@ input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 521 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ +input.cpp:545:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 545 | if ( gn != 2 * include.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~~ +input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 579 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 595 | 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] + 631 | for (int i=0; i >&)': +helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 58 | for (int i=0; i >&)': +helper.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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 76 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 79 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 90 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +helper.cpp: In function 'void display(std::vector&)': +helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 100 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +input.cpp: In member function 'void Plink::readSet()': +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] + 193 | for (int t=0; t::size_type' {aka 'unsigned int'} [-Wsign-compare] + 787 | for (int i=0; i > CArgs::value(std::string, int)': +helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 267 | if ( (i+j) < a.size() ) + | ~~~~~~^~~~~~~~~~ +helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); + | ~~~~~~~~~^~~~ +helper.cpp: In function 'std::vector > parse2str(std::string)': +helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 306 | for (int i=0 ; i < s.length() ; i++) + | ~~^~~~~~~~~~~~ +helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 307 | if (s[i] == ',' || i == s.length()-1 ) + | ~~^~~~~~~~~~~~~~~ +helper.cpp:309:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 309 | if (i == s.length()-1) t += s[i]; + | ~~^~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector parse2int(std::string)': +helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 323 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 545 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 218 | 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] - 579 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_twolocus()': -output.cpp:402:28: warning: variable 'loc1' set but not used [-Wunused-but-set-variable] - 402 | vector::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; - | ^~~~ 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++) | ~~^~~~~~~~~~~~~~ -input.cpp:595:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 595 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 309 | 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] - 631 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -cluster.cpp: In member function 'void Plink::buildCluster()': -cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 272 | for (int z=1; z<=qt.size(); z++) - | ~^~~~~~~~~~~ -In file included from helper.h:24, - from stats.cpp:30: +In file included from plink.cpp:28: 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::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'} and 'int' [-Wsign-compare] + 817 | if (tokens.size() < 2+par::mult_clst) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 821 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] + 897 | 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() ) | ~~~^~~~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readSet()': -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] + 461 | for (int i=1; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 927 | for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 961 | else if ( ccount != tokens.size() ) + | ~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 965 | if (tokens.size() < 2+par::mult_pheno) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1043 | 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from epi.cpp:23: +input.cpp: In member function 'void Plink::makePhenotype()': +input.cpp:1208:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1208 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1232 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1256 | if (tokens.size() < 2+par::mult_covar) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1261 | for (int i0=0; i0freq * ( 1 - locus[l]->freq ); + | ^~ +helper.cpp: In function 'void summaryBasics(Plink&)': +helper.cpp:595:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 595 | 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] + 659 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 664 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1335 | for (int i=0; i > listPossibleHaplotypes(Plink&, std::vector)': +helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 709 | while(h >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 729 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] + 775 | for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': +helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 795 | for (int s = 0 ; s < snps.size() ; s++) + | ~~^~~~~~~~~~~~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': -genome.cpp:99:15: warning: unused variable 'geno_nm' [-Wunused-variable] - 99 | int geno_nm = 0; - | ^~~~~~~ -genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] - 81 | double tothet = 0; - | ^~~~~~ -In file included from phase.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] - 787 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 452 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 511 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 952 | if ( c < 0 || c >= par::chr_code.size() ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': +helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 959 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 966 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 973 | for (int l=0;l >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector getChromosomeMarkerRange(Plink&, int)': +helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 989 | for (int i=0;i getChromosomeRange(Plink&)': +helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1040 | for (int i=0;i >)': +helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1172 | for (int k=0; k::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1264 | if (sample[i]->fid.length() > par::pp_maxfid) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1267 | if (sample[i]->iid.length() > par::pp_maxiid) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1273 | if (locus[l]->name.length() > par::pp_maxsnp) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1391 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1227 | for (int i=0;i::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] 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] + 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1572 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1599 | else if (tokens.size() != par::plist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1602 | 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] + 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1792 | 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++ ) + | ~~^~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2225 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +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; + | ^ +input.cpp: In member function 'void Plink::readFamFile(std::string)': +input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i&)': +helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] + 2204 | int i = 0; + | ^ +input.cpp: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': +input.cpp:2471:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2471 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2455 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2462 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2491 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2510 | for (int i=0; i > msqrt(std::vector >&)': +stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] + 906 | const double eps = 1e-12; + | ^~~ +helper.cpp: In member function 'void Plink::filterOnControl()': +helper.cpp:2530:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2530 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2549 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2568 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2587 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2606 | 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] + 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] + 2638 | for (int i=0; i::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] + 1477 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1483 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1515 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1521 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp: In function 'matrix_t vec2diag(vector_t&)': +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++) + | ~~^~~~~~~~~~ +filters.cpp: In member function 'void Plink::thinSNPs()': +filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] + 1277 | int x = 0; + | ^ +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::size_type' {aka 'unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2722 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2756 | for (int j=1; j, Individual*>&)': +helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2935 | for (int i=0; i&)': +helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 2959 | if ( input.size() != P.nl_all ) + | ~~~~~~~~~~~~~^~~~~~~~~~~ +helper.cpp: In function 'std::map, std::set > readRange(std::string)': +helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] + 3097 | set * s; + | ^ +plink.cpp: In function 'int main(int, char**)': +plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 763 | par::make_founders && + | ~~~~~~~~~~~~~~~~~~~^~ + 764 | !par::built_families) + | ~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp +helper.cpp: In function 'void makeScaffold(Plink&)': +helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] + 3324 | int last = -1; + | ^~~~ +helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] + 3328 | int thisChromosome = P.locus[0]->chr; + | ^~~~~~~~~~~~~~ +helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] + 3329 | int nextChromosome; + | ^~~~~~~~~~~~~~ +plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2359 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2362 | for (int l=0; l::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++) + | ~~^~~~~~~~~~~~~~~~~~ +multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': +multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 295 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 304 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 357 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 372 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +cluster.cpp: In member function 'void Plink::buildCluster()': +cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 272 | for (int z=1; z<=qt.size(); z++) + | ~^~~~~~~~~~~ +cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 452 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 511 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 651 | for (int i=0;i::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'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::calcFst()': -genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] - 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); - | ^~ cluster.cpp:784:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 784 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 786 | for (int j=0;j >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 817 | if (tokens.size() < 2+par::mult_clst) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 821 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] - 897 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 927 | for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 961 | else if ( ccount != tokens.size() ) - | ~~~~~~~^~~~~~~~~~~~~~~~ -input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 965 | if (tokens.size() < 2+par::mult_pheno) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -filters.cpp:273:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 273 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1043 | 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] 919 | for (int k=0;k >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -filters.cpp:591:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 591 | for (int i=0; i::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -filters.cpp:611:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1208 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 954 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 976 | for (int j=i+1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1232 | for (int i=0; i::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': -genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] - 843 | double e10 = E10*S; - | ^~~ -genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] - 844 | double e20 = E20*S; - | ^~~ -genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] - 848 | double e21 = E21*S; - | ^~~ -In file included from trio.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++) - | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1256 | if (tokens.size() < 2+par::mult_covar) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1261 | for (int i0=0; i0 >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from prephap.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&, std::vector&, std::vector >&)': -stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] - 458 | int m,l,iter,i,k; - | ^ cluster.cpp:1049:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1049 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1061 | for (int j2=0; j2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1107 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1335 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1163 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 146 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] - 154 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int e=0;e >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ -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++ ) - | ~~^~~~~~~~~~~~~~ -tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': -tdt.cpp:81:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 81 | for (int i=0; iperson.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -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++ ) - | ~~^~~~~~~~~~~~~~~ cluster.cpp: In function 'double cldist(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1203 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1204 | for (int j=0; jperson[i]; - | ^~~~~~ cluster.cpp: In function 'double groupAvgLink(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1228 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1229 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 132 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 144 | for (int c=0; c < fam->kid.size(); c++) - | ~~^~~~~~~~~~~~~~~~~ cluster.cpp: In function 'bool homogeneous_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1254 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1255 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 210 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 234 | for (int f=0; f >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 327 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::groupGenome()': cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1661 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ 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::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1477 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': -phase.cpp:373:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 373 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1483 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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); + | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp +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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2200 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2322 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2367 | for (int i=0; i < setname.size();i++) + | ~~^~~~~~~~~~~~~~~~ +output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2380 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2409 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2412 | for (int l=0; l >::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::difference_type)' at /usr/include/c++/14/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++/14/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++/14/bits/stl_bvector.h:385:24, + inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_bvector.h:1087:23, + inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: +/usr/include/c++/14/bits/stl_bvector.h:229:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] + 229 | __n = __n % int(_S_word_bit); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1405:11: note: 'maxI' was declared here + 1405 | int maxI; + | ^~~~ +In file included from helper.h:24, + from assoc.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 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from assoc.cpp:29: +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] + 395 | for (int i=0; iprofileSNPs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~ +epi.cpp: In member function 'void Plink::calcEpistasis()': +epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 146 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] + 154 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] + 741 | for (int j=0; jselectedSNPs[l].size(); j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 785 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:51, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from cluster.cpp:14: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 788 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +epi.cpp:438:26: warning: unused variable 'zero' [-Wunused-variable] + 438 | double zero = 0; + | ^~~~ +epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] + 701 | int c=0; + | ^ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] + 1536 | int best = 0 ; + | ^~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::display_pairList()': +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; + | ^~ +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; + | ^~ +In file included from prephap.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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 226 | if (len != tokens.size() - offset ) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1515 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1521 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp: In function 'matrix_t vec2diag(vector_t&)': -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++) - | ~~^~~~~~~~~~ -phase.cpp: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': -phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 472 | while (h >::size_type' {aka 'unsigned int'} [-Wsign-compare] 283 | for ( int i = allele ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ -tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 412 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -phase.cpp: In member function 'void HaploPhase::performAlternEM()': -phase.cpp:678:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 678 | for (int z=0; z::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 >&)': -helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 58 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 412 | while ( index < tokens.size() ) | ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 416 | if ( tokens[index].size() != len ) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ -helper.cpp: In function 'std::string displayLine(std::vector >&)': -helper.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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'void display(matrix_t&)': -helper.cpp:76:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 76 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 79 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 90 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -helper.cpp: In function 'void display(std::vector&)': -helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 100 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -filters.cpp:1165:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1165 | for ( int i=0; i 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::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 557 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 668 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 776 | for (int f=0; f >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1599 | else if (tokens.size() != par::plist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1187 | if ( nh != hapmap.size() ) - | ~~~^~~~~~~~~~~~~~~~ -phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1238 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 470 | for (int s=0;s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1280 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1792 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1299 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 560 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from phase.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] - 91 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~ -helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': -helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 193 | for (int t=0; t&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2116 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2172 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2200 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2210 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2225 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -helper.cpp: In member function 'std::vector > CArgs::value(std::string, int)': -helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 267 | if ( (i+j) < a.size() ) - | ~~~~~~^~~~~~~~~~ -helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); - | ~~~~~~~~~^~~~ +phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': +phase.cpp:373:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 373 | for (int i=0; i&)': +phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 472 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] + 678 | for (int z=0; z, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1187 | if ( nh != hapmap.size() ) + | ~~~^~~~~~~~~~~~~~~~ +phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1238 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1280 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1299 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) | ~~^~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector > parse2str(std::string)': -helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 306 | for (int i=0 ; i < s.length() ; i++) - | ~~^~~~~~~~~~~~ -helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 307 | if (s[i] == ',' || i == s.length()-1 ) - | ~~^~~~~~~~~~~~~~~ -helper.cpp:309:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 309 | if (i == s.length()-1) t += s[i]; - | ~~^~~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector parse2int(std::string)': -helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 323 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 395 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1829 | for (int z=0; z < hap1[i].size(); z++) @@ -1162,26 +1454,25 @@ phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ -helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': -helper.cpp:461:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 461 | for (int i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 741 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 785 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::updateAlleles()': -input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] - 2732 | bool success = false; - | ^~~~~~~ -assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 788 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ +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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp +In file included from trio.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++) + | ~~^~~~~~~~~~~~~~~~~~ +trio.cpp: In function 'void addPerson(Family*, Individual*)': +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++) + | ~^~~~~~~~~~~~~~ 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++) @@ -1189,82 +1480,15 @@ trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 272 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ -In file included from plink.cpp:35: -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] - 2200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 595 | 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] 335 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'double genotypingRate(Plink&, int)': -helper.cpp:659:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 659 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 664 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 342 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 350 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ -output.cpp:2322:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2322 | for (int j=0; j > listPossibleHaplotypes(Plink&, std::vector)': -helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 709 | while(h >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2367 | for (int i=0; i < setname.size();i++) - | ~~^~~~~~~~~~~~~~~~ -helper.cpp:729:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 729 | for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2380 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 775 | for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': -helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 795 | for (int s = 0 ; s < snps.size() ; s++) - | ~~^~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::writeSetFile()': -output.cpp:2409:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2409 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2412 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 952 | if ( c < 0 || c >= par::chr_code.size() ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': -helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 959 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 966 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 469 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 474 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 973 | for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] 492 | for (int f=0; f getChromosomeMarkerRange(Plink&, int)': -helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 989 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 504 | for (int c=0; c getChromosomeRange(Plink&)': -helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1040 | for (int i=0;i >)': -helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1172 | for (int k=0; k::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1264 | if (sample[i]->fid.length() > par::pp_maxfid) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1267 | if (sample[i]->iid.length() > par::pp_maxiid) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1273 | if (locus[l]->name.length() > par::pp_maxsnp) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1391 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 871 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 936 | for (int f=0;f Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] - 1536 | int best = 0 ; - | ^~~~ trio.cpp:943:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 943 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:13: warning: unused variable 'tmp' [-Wunused-variable] 962 | int tmp = deleteIndividuals(indel); | ^~~ -In file included from perm.h:17, - from sharing.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++) - | ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1038 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': -helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] - 2204 | int i = 0; - | ^ -helper.cpp: In member function 'void Plink::filterOnCovariate()': -helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2455 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2462 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2491 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2510 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2530 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2549 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2568 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2587 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2606 | 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; + | ^~~~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': +tdt.cpp:81:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 81 | for (int i=0; iperson.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:96:30: warning: unused variable 'person' [-Wunused-variable] + 96 | Individual * person = klist[k]->person[i]; + | ^~~~~~ +tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 132 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 144 | for (int c=0; c < fam->kid.size(); c++) + | ~~^~~~~~~~~~~~~~~~~ +tdt.cpp:210:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 210 | for (int i=0; iprofileSNPs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 234 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 327 | for (int j=0; jselectedSNPs[l].size(); j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 412 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~~~~~ +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::size_type' {aka 'unsigned int'} [-Wsign-compare] + 557 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 668 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 776 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': 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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2638 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2671 | for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2722 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: +/usr/include/c++/14/ostream:229:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 229 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1385:22: note: 'mult_chisq' was declared here + 1385 | double mult_p, mult_chisq; + | ^~~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: +/usr/include/c++/14/ostream:229:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 229 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:14: note: 'dom_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: +/usr/include/c++/14/ostream:229:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 229 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:25: note: 'rec_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: +/usr/include/c++/14/ostream:229:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 229 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:36: note: 'gen_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +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; + | ^~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp -plink.cpp: In member function 'void Plink::cleanUp()': -plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2359 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2362 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2366 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2756 | for (int j=1; j, Individual*>&)': -helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2935 | for (int i=0; i&)': -helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 2959 | if ( input.size() != P.nl_all ) - | ~~~~~~~~~~~~~^~~~~~~~~~~ -helper.cpp: In function 'std::map, std::set > readRange(std::string)': -helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] - 3097 | set * s; - | ^ -helper.cpp: In function 'void makeScaffold(Plink&)': -helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] - 3324 | int last = -1; - | ^~~~ -helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] - 3328 | int thisChromosome = P.locus[0]->chr; - | ^~~~~~~~~~~~~~ -helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] - 3329 | int nextChromosome; - | ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp -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); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'int CArgs::value_int(std::string)': -helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] - 231 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': -helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] - 243 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'double CArgs::value_double(std::string)': -helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] - 255 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In function 'int getInt(std::string, std::string)': -helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] - 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': -helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] - 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -helper.cpp: In function 'double getDouble(std::string, std::string)': -helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] - 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.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] @@ -1526,6 +1687,11 @@ genepi.cpp:507:17: warning: unused variable 'ne' [-Wunused-variable] 507 | int ne = n1 < n2 ? n1 : n2; | ^~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': genepi.cpp:1025:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1025 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: 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] @@ -1613,13 +1767,6 @@ sets.cpp:332:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 332 | for (int k=j+1; k < snpset[i].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] 367 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -perm.cpp: In member function 'void Perm::setOriginalRanking(vector_t&)': -perm.cpp:187:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 618 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >::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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp 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::size_type' {aka 'unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from gxe.cpp:20: +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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from merge.cpp:22: +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]; + | ^ +genepi.cpp:614:17: note: 'cancor1_pos' was declared here + 614 | int cancor1_pos; + | ^~~~~~~~~~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~ merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 333 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 842 | for (int i=0; i::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp -In file included from /usr/include/c++/14/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]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: -/usr/include/c++/14/ostream:229:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 229 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1385:22: note: 'mult_chisq' was declared here - 1385 | double mult_p, mult_chisq; - | ^~~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: -/usr/include/c++/14/ostream:229:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 229 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:14: note: 'dom_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: -/usr/include/c++/14/ostream:229:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 229 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:25: note: 'rec_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: -/usr/include/c++/14/ostream:229:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 229 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:36: note: 'gen_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp -In file included from hotel.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++) - | ~~^~~~~~~~~~~~~~~~~~ -hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': -hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 77 | if (!sample[i]->missing) - | ^ -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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 85 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': +hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 77 | if (!sample[i]->missing) + | ^ +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 >::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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp -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]; - | ^ -genepi.cpp:614:17: note: 'cancor1_pos' was declared here - 614 | int cancor1_pos; - | ^~~~~~~~~~~ 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] @@ -1938,48 +1993,32 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp -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++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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++) | ~~^~~~~~~~~~~~~~~~~~ -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 > >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 195 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 198 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ -poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': -poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 293 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 328 | for (int c=0; c >::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++) | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 117 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 180 | if ( i < tokens.size() - 1) | ~~^~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 218 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 93 | for (int f=0; f > >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 195 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 198 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ +poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': +poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 293 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 328 | for (int c=0; c, int>&)': +merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] + 1103 | if (write) + | ^~ +merge.cpp:943:8: note: 'write' was declared here + 943 | bool write; + | ^~~~~ +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 helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -2044,34 +2115,38 @@ linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 50 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::difference_type)' at /usr/include/c++/14/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++/14/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++/14/bits/stl_bvector.h:385:24, - inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_bvector.h:1087:23, - inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: -/usr/include/c++/14/bits/stl_bvector.h:229:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] - 229 | __n = __n % int(_S_word_bit); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1405:11: note: 'maxI' was declared here - 1405 | int maxI; - | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp +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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -2109,30 +2184,14 @@ bmerge.cpp:883:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 883 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ -merge.cpp:943:8: note: 'write' was declared here - 943 | bool write; - | ^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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()': 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: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++) - | ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 368 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | 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] - 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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.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) { @@ -2204,14 +2246,12 @@ 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp In file included from helper.h:24, from homozyg.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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 673 | for (int i=0; i < plist.size(); i++) @@ -2253,18 +2293,20 @@ 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; +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp +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 helper.h:24, from segment.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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.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++) - | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2292,15 +2334,15 @@ segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; ifirst; | ^ +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++) + | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] 2003 | int nseg = smap.size(); @@ -2342,6 +2384,12 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp +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 ) @@ -2360,6 +2408,12 @@ model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp +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"); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 1882 | if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; @@ -2368,13 +2422,6 @@ dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; | ~~~~~~^~~~~~~~~~~~~~ -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; - | ^~~~ dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); @@ -2403,14 +2450,12 @@ dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp 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::size_type' {aka 'unsigned int'} [-Wsign-compare] 423 | for (int c=0; c::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: +/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bmerge.cpp: In member function 'void Plink::mergeBinaryData()': +bmerge.cpp:682:16: note: 'indn' was declared here + 682 | int indn; + | ^~~~ +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] 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp -In file included from dfam.cpp:23: +dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': +dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 76 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 86 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 96 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 106 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 157 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 271 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 378 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] + 218 | bool informative = false; + | ^~~~~~~~~~~ +dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 504 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] + 151 | int totalInformative = 0; + | ^~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from elf.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++) | ~~^~~~~~~~~~~~~~~~~~ +elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': +elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 493 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': +elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 609 | for (int l=0; l< original.size(); l++) + | ~^~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': +elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] + 654 | const double pthresh = 0.01; + | ^~~~~~~ +elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] + 655 | bool one_sided = true; + | ^~~~~~~~~ +elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] + 707 | int srange_cnt = 0; + | ^~~~~~~~~~ +elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] + 708 | bool inRange = false; + | ^~~~~~~ +elf.cpp: In member function 'void Plink::displayRareRange()': +elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 895 | for (int i = 0 ; i < tokens.size() ; i++) + | ~~^~~~~~~~~~~~~~~ +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 ) + | ~~~~~~~~~~~~~~^~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp +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; + | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp In file included from helper.h:24, - from elf.cpp:19: + from fisher.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++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 261 | prterr(1, "NROW must be less than or equal to LDTABL."); @@ -2543,88 +2673,6 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': -dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 76 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 86 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 96 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 106 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 157 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 271 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 378 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] - 218 | bool informative = false; - | ^~~~~~~~~~~ -dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 504 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] - 151 | int totalInformative = 0; - | ^~~~~~~~~~~~~~~~ -elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': -elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 493 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': -elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 609 | for (int l=0; l< original.size(); l++) - | ~^~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': -elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] - 654 | const double pthresh = 0.01; - | ^~~~~~~ -elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] - 655 | bool one_sided = true; - | ^~~~~~~~~ -elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] - 707 | int srange_cnt = 0; - | ^~~~~~~~~~ -elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] - 708 | bool inRange = false; - | ^~~~~~~ -elf.cpp: In member function 'void Plink::displayRareRange()': -elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 895 | for (int i = 0 ; i < tokens.size() ; i++) - | ~~^~~~~~~~~~~~~~~ -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 ) - | ~~~~~~~~~~~~~~^~~~~~~ -In file included from helper.h:24, - from sockets.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++) - | ~~^~~~~~~~~~~~~~~~~~ -sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': -sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] - 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request - | ^~~~~~~ -sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] - 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response - | ^~~~~~ -sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] - 81 | unsigned int i; // Loop counter - | ^ -sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] - 119 | int echoStringLen = 100; - | ^~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.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] @@ -2652,18 +2700,18 @@ linput.cpp:209:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 209 | for (int i=0; i >::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 sockets.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++) + | ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 206 | for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 289 | for (int i=25; i > socketConnection(Plink*, std::string, int, std::string)': +sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] + 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request + | ^~~~~~~ +sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] + 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response + | ^~~~~~ +sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] + 81 | unsigned int i; // Loop counter + | ^ +sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] + 119 | int echoStringLen = 100; + | ^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp +elf.cpp: In member function 'bool RCount::addSNP(int)': +elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] + 374 | double wt; + | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from pdriver.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] @@ -2695,6 +2763,7 @@ 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] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2727,14 +2795,25 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ +elf.cpp: In member function 'void Plink::elfBaseline()': +elf.cpp:1159:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] + 1159 | ++(*p_cnt); + | ~^~~~~~~ +elf.cpp:1111:13: note: 'p_cnt' was declared here + 1111 | int * p_cnt; + | ^~~~~ +elf.cpp:1153:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] + 1153 | ++(*p_gcnt); + | ~^~~~~~~~ +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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from haploQTL.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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp In file included from haploQTL.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] @@ -2747,31 +2826,7 @@ 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++) | ~~^~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp -In file included from /usr/include/i386-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from bmerge.cpp:14: -In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: -/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bmerge.cpp: In member function 'void Plink::mergeBinaryData()': -bmerge.cpp:682:16: note: 'indn' was declared here - 682 | int indn; - | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.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] @@ -2813,15 +2868,15 @@ haplohelper.cpp:413:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 413 | for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] - 487 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +haplohelper.cpp: In member function 'void HaploPhase::reportPhaseWideFormat()': +haplohelper.cpp:487:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 487 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 655 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: 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] @@ -2904,20 +2954,6 @@ haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 183 | while (h >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::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] 558 | for (int z=0; z < hap1[i].size(); z++) @@ -2954,19 +2990,33 @@ 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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from genogroup.cpp:24: +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] + 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] 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.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] @@ -2976,17 +3026,34 @@ 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++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:28: 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] + 668 | for (int z=0; z < pp[i].size(); z++) + | ~~^~~~~~~~~~~~~~ +nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] + 360 | int pcnt=1; + | ^~~~ In file included from clumpld.cpp:21: 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&)': +nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] + 715 | double posterior = ip->second; + | ^~~~~~~~~ clumpld.cpp: In member function 'std::vector clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 92 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -nonfounderphasing.cpp: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': -nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 668 | for (int z=0; z < pp[i].size(); z++) - | ~~^~~~~~~~~~~~~~ -nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] - 360 | int pcnt=1; - | ^~~~ -nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': -nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] - 715 | double posterior = ip->second; - | ^~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) @@ -3027,52 +3083,21 @@ clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | if( l1 < P->locus.size()-1 ) | ~~~^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ -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; - | ^~~ -elf.cpp: In member function 'bool RCount::addSNP(int)': -elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] - 374 | double wt; - | ^~ 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp -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++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 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] @@ -3082,45 +3107,16 @@ 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] - 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] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 105 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 157 | for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 189 | for( int a = 0; a < posshap1.size(); a++ ) | ~~^~~~~~~~~~~~~~~~~ @@ -3130,16 +3126,38 @@ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 225 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ -impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -impute.cpp: In member function 'void HaploPhase::mainImputation()': -impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 313 | for (int s=0; s < g.size(); s++) - | ~~^~~~~~~~~~ +genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 315 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 328 | for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] + 347 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +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 >::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] 166 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 315 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] - 347 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -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 >::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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp -In file included from metaem.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] + 105 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp: In member function 'void HaploPhase::mainImputation()': +impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 313 | for (int s=0; s < g.size(); s++) + | ~~^~~~~~~~~~ +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] + 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] @@ -3203,6 +3243,35 @@ metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 239 | while (h::difference_type)' at /usr/include/c++/14/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++/14/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++/14/bits/stl_bvector.h:385:24, + inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_bvector.h:1087:23, + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: +/usr/include/c++/14/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; + | ^~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from nlist.h:21, + from nlist.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++) + | ~~^~~~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; @@ -3228,27 +3297,6 @@ profile.cpp:421:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ -profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': -profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] - 480 | bool a1 = i2->second; - | ^~ -profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] - 525 | bool sawNamedAllele = false; - | ^~~~~~~~~~~~~~ -profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': -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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 38 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ +profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': +profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] + 480 | bool a1 = i2->second; + | ^~ +profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] + 525 | bool sawNamedAllele = false; + | ^~~~~~~~~~~~~~ +profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': +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 >::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 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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.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); - | ~^~~~~~~ -elf.cpp:1111:13: note: 'p_cnt' was declared here - 1111 | int * p_cnt; - | ^~~~~ -elf.cpp:1153:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] - 1153 | ++(*p_gcnt); - | ~^~~~~~~~ -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.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++) + | ~~^~~~~~~~~~~~~~~~~~ +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] 252 | for (int i=0; i::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::size_type' {aka 'unsigned int'} [-Wsign-compare] + 125 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) @@ -3319,6 +3406,9 @@ whap.cpp:456:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 456 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] + 192 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ +gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 247 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 298 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 381 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 395 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 403 | for (int i=0; isecond; + | ^~ +gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] + 414 | bool fatal = false; + | ^~~~~ +gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 549 | 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] + 556 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ @@ -3389,84 +3508,16 @@ whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ -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 >::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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 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++) | ~~^~~~~~~~~~~~~~~~~~ -gvar.cpp: In member function 'void Plink::readGenericVariantData()': -gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 125 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 192 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 247 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 298 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 381 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 395 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 403 | for (int i=0; isecond; - | ^~ -gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] - 414 | bool fatal = false; - | ^~~~~ -gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 549 | 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] - 556 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ @@ -3507,7 +3552,12 @@ cnv.cpp:1103:43: warning: variable 'il' set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 step.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++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ @@ -3538,29 +3588,11 @@ 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp -In file included from /usr/include/c++/14/vector:67, - from options.h:18: -In member function 'void std::_Bit_iterator_base::_M_incr(std::ptrdiff_t)', - inlined from 'std::_Bit_iterator::iterator& std::_Bit_iterator::operator+=(std::iterator::difference_type)' at /usr/include/c++/14/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++/14/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++/14/bits/stl_bvector.h:385:24, - inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_bvector.h:1087:23, - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: -/usr/include/c++/14/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; - | ^~~ In file included from greport.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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 78 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 169 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 240 | for (int l=0; l< ari->second.size(); l+=2) | ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 flip.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3596,16 +3628,21 @@ 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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.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++) | ~~^~~~~~~~~~~~~~~~~~ -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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp In file included from cfamily.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] @@ -3631,7 +3668,24 @@ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp +In file included from setscreen.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++) + | ~~^~~~~~~~~~~~~~~~~~ +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'} and 'int' [-Wsign-compare] + 110 | if ( tokens.size() != cols ) + | ~~~~~~~~~~~~~~^~~~~~~ +setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) + | ~~^~~~~~~~~~~~~~~~~~~ +setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': @@ -3650,6 +3704,12 @@ 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 >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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++) @@ -3690,6 +3750,7 @@ idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 547 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ @@ -3813,11 +3874,6 @@ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1440 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from setscreen.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++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1551 | for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp 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) @@ -3885,7 +3942,6 @@ idhelp.cpp:2024:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2024 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2030 | if ( maxF >= tok.size() ) | ~~~~~^~~~~~~~~~~~~ @@ -3895,20 +3951,6 @@ idhelp.cpp:2070:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ -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'} and 'int' [-Wsign-compare] - 110 | if ( tokens.size() != cols ) - | ~~~~~~~~~~~~~~^~~~~~~ -setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) - | ~~^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp -setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int i=0; i < snpset[j].size(); i++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -3931,12 +3973,6 @@ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp 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 helper.h:24, from hapglm.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] @@ -3947,7 +3983,6 @@ 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 >::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++) + | ~~^~~~~~~~~~~~~~~~~~ blox.cpp: In member function 'std::map > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; @@ -3998,12 +4036,6 @@ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 418 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ blox.cpp:427:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 427 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -4024,11 +4057,11 @@ 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] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp 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] ) +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp 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; q >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -4089,67 +4147,6 @@ annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] 300 | bool include = false; | ^~~~~~~ -In file included from Rconnection.cpp:30: -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(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -In file included from helper.h:24, - from r.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++) - | ~~^~~~~~~~~~~~~~~~~~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -Rconnection.cpp: At global scope: -Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ - | ^~~~~~~~~~~~~~ -Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': -Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 567 | if (host) free(host); host=0; - | ^~ -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 r.cpp:29: -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(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -r.cpp: In member function 'void Plink::Rfunc()': -r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] - 330 | int ct = data->length(); - | ^~ In file included from metaanal.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] @@ -4199,30 +4196,69 @@ metaanal.cpp:680:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 680 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from r.cpp:29: +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(); } + | ^~ +Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': +Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 206 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In member function 'char* Rstrings::stringAt(int)': +Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +r.cpp: In member function 'void Plink::Rfunc()': +r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] + 330 | int ct = data->length(); + | ^~ +In file included from Rconnection.cpp:30: +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(); } + | ^~ +Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': +Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 206 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In member function 'char* Rstrings::stringAt(int)': +Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +Rconnection.cpp: At global scope: +Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ + | ^~~~~~~~~~~~~~ +Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': +Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 567 | if (host) free(host); host=0; + | ^~ +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; + | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -4306,12 +4342,14 @@ 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/27197/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27197/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/64070 and its subdirectories -I: Current time: Fri Feb 27 10:38:09 -12 2026 -I: pbuilder-time-stamp: 1772231889 +I: removing directory /srv/workspace/pbuilder/27197 and its subdirectories +I: Current time: Sun Jan 26 06:18:59 +14 2025 +I: pbuilder-time-stamp: 1737821939