Diff of the two buildlogs: -- --- b1/build.log 2025-11-17 20:41:49.394241335 +0000 +++ b2/build.log 2025-11-17 20:44:04.890408439 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 20 15:02:25 -12 2026 -I: pbuilder-time-stamp: 1797822145 +I: Current time: Tue Nov 18 10:41:50 +14 2025 +I: pbuilder-time-stamp: 1763412110 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying gcc11.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3901677/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3252757/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 17 20:41 /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/3252757/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3252757/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='203a83d4167a48dba9535c920e97d8c7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3901677' - PS1='# ' - PS2='> ' + INVOCATION_ID=cf8ee417fae646b68699a30b9244a791 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3252757 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.X5g6BGvw/pbuilderrc_Dyg4 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.X5g6BGvw/b1 --logfile b1/build.log plink_1.07+dfsg-5.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - 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.X5g6BGvw/pbuilderrc_zP7H --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.X5g6BGvw/b2 --logfile b2/build.log plink_1.07+dfsg-5.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + 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 ionos15-amd64 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3901677/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3252757/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.2 MB in 1s (9880 kB/s) +Fetched 12.2 MB in 1s (9215 kB/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 ... 19862 files and directories currently installed.) @@ -282,7 +314,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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-5_source.changes +I: user script /srv/workspace/pbuilder/3252757/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3252757/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-5_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -294,7 +330,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j42 clean + make -j40 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' @@ -309,7 +345,7 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 - make -j42 INSTALL="install --strip-program=true" CXXFLAGS="-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 + make -j40 INSTALL="install --strip-program=true" CXXFLAGS="-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp @@ -351,19 +387,12 @@ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from sets.cpp:24: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? 15 | #define __HAPPHASE_H__ -In file included from haploTDT.cpp:25: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from plink.cpp:35: +In file included from haploCC.cpp:25: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? @@ -383,12 +412,12 @@ 13 | #ifndef __HAPWINDOW_H_ haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? 14 | #define __HAPWINDOW_H__ -In file included from haploCC.cpp:25: +In file included from haploTDT.cpp:25: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? 15 | #define __HAPPHASE_H__ -In file included from mishap.cpp:20: +In file included from plink.cpp:35: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? @@ -403,272 +432,70 @@ 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? 15 | #define __HAPPHASE_H__ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp +In file included from mishap.cpp:20: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ 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 'long 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from webcheck.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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long 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 'long unsigned int'} [-Wsign-compare] - 80 | for ( int i = 4; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 105 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 117 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 130 | if ( i < tokens.size()-1 ) - | ~~^~~~~~~~~~~~~~~~~ -webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | if ( i < tokens.size()-1 ) - | ~~^~~~~~~~~~~~~~~~~ -webcheck.cpp:180:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 180 | if ( i < tokens.size() - 1) - | ~~^~~~~~~~~~~~~~~~~~~ -webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 218 | for (int i=0; i >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp -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 'long unsigned int'} [-Wsign-compare] - 102 | for (int l=0; l >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long 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 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploTDT.cpp:24: +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 'long 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 'long unsigned int'} [-Wsign-compare] - 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 64 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 86 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from phase.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 'long 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()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -tinput.cpp: In member function 'void Plink::readTransposedData()': -tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 271 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ +genedrop.cpp: In member function 'void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector&, std::vector&, std::vector&, std::map&)': +genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 340 | for (int k=0; kkids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 309 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from multiple.cpp:22: +In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 516 | if ( i == include.size() ) - | ~~^~~~~~~~~~~~~~~~~ -input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 545 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 368 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 377 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 591 | if ( c > sample.size()) - | ~~^~~~~~~~~~~~~~~ -input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 579 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 381 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ -input.cpp:595:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 384 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -legacy.cpp:390:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 390 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 611 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -legacy.cpp:395:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 395 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 631 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 415 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 424 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from mishap.cpp:17: +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -677,6 +504,25 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 95 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 123 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 132 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 155 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 163 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 198 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 37 | for(int s=0;s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 62 | if (par::set_max==-1 || par::set_max > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -legacy.cpp:460:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 460 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 461 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 462 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -legacy.cpp:467:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 467 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 480 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 190 | for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 191 | for (int i2=0; i2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 99 | for(int i=0;i 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 'long unsigned int'} [-Wsign-compare] - 295 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 304 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 117 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 130 | if ( i < tokens.size()-1 ) + | ~~^~~~~~~~~~~~~~~~~ +webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 146 | if ( i < tokens.size()-1 ) + | ~~^~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneMC(Plink&, bool, double)': sets.cpp:129:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 129 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 357 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 372 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 180 | if ( i < tokens.size() - 1) + | ~~^~~~~~~~~~~~~~~~~~~ sets.cpp:176:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 95 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 123 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 132 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 155 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 163 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 216 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 198 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, - from helper.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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~ -In file included from genepi.cpp: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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -multi.cpp:154:8: warning: unused variable 'is0zero' [-Wunused-variable] - 154 | bool is0zero = IBDg.z0 < EPS ? true : false; - | ^~~~~~~ -multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] - 155 | bool is1zero = IBDg.z1 < EPS ? true : false; - | ^~~~~~~ -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; - | ^~~~~~ -genedrop.cpp: In member function 'void Perm::preGeneDrop()': -genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 64 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 273 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -819,10 +603,6 @@ sets.cpp:237:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 237 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 520 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 317 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -output.cpp:526:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 526 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 332 | for (int k=j+1; k < snpset[i].size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -output.cpp:553:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 553 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -linear.cpp: In member function 'virtual void LinearModel::pruneY()': -linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 367 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 370 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] - 249 | double freq; - | ^~~~ -filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] - 250 | int nm; - | ^~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 412 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'bool Plink::readClusterFile(bool)': -input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 787 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 611 | for (int i=0; ifreq * ( 1 - locus[l]->freq ); - | ^~ -In file included from plink.cpp:28: +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 85 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 191 | for (int i2=0; i2::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 131 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 821 | for (int i0=0; i0 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int l=0; l::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 762 | for ( int i = 0 ; i < sample.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 618 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | for (int j=0;j&, std::vector&, std::vector&, std::map&)': -genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 340 | for (int k=0; kkids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~ sets.cpp:631:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 631 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 643 | for (int j=0;j >&)': +helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 703 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 897 | for (int i=0; i::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 762 | for ( int i = 0 ; i < sample.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -linear.cpp: In member function 'double LinearModel::getPValue()': -linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] - 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; - | ^~~~ -input.cpp:927:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 927 | for ( int i=2; i >::size_type' {aka 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] - 965 | if (tokens.size() < 2+par::mult_pheno) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1043 | for (int i=0; imissing) - | ^ -input.cpp:1064:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1064 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 81 | for (int i=0; iperson.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from perm.h:17, - from perm.cpp:17: +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 'long 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 'long unsigned int'} [-Wsign-compare] + 79 | for (int j=0; j::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 100 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 132 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -tdt.cpp:144:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | for (int c=0; c < fam->kid.size(); c++) - | ~~^~~~~~~~~~~~~~~~~ -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; - | ^ -hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 173 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 210 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] - 848 | double e21 = E21*S; - | ^~~ -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 'long unsigned int'} [-Wsign-compare] - 1208 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 234 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 93 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1232 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 713 | for (int j=0; j >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 1261 | for (int i0=0; i0 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -mds.cpp:279:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -qfam.cpp: In function 'void scoreBetween(Plink&, int)': -qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 82 | for (int k=0; k < (*f)->kid.size() ;k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': -genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 1067 | if ( (!par::silent ) && c==c2 || c==np) - | ~~~~~~~~~~~~~~~~^~~~~~~~ -qfam.cpp:89:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': -stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] - 813 | const double eps = 1e-12; - | ^~~ -stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] - 818 | int r = u.size(); - | ^ -tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 97 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -stats.cpp: In function 'std::vector > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ -input.cpp: In member function 'bool Plink::readCovListFile()': -input.cpp:1335:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 267 | for (int i=0; i < family.size(); i++) - | ~~^~~~~~~~~~~~~~~ -poo.cpp:195:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 198 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::pruneLD()': -genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1078 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1091 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 91 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~ -binput.cpp:261:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | while (s > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 412 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -binput.cpp:339:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 339 | while (s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 415 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ -binput.cpp:351:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ filters.cpp:1143:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1143 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ filters.cpp:1165:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1165 | for ( int i=0; i >&)': -helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 58 | for (int i=0; i::size_type' {aka 'long 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 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] - 1521 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i 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 'long unsigned int'} [-Wsign-compare] - 293 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] + 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); + | ~~~~~~~~~^~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long 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 'long unsigned int'} [-Wsign-compare] + 307 | if (s[i] == ',' || i == s.length()-1 ) + | ~~^~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 295 | for (int i=0;i::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 323 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 304 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 357 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 372 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1531 | for (int i = 0; i < v.size(); i++) - | ~~^~~~~~~~~~ -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 'long 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 'long unsigned int'} [-Wsign-compare] - 79 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 90 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -input.cpp:1374:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 315 | for (int f = 0 ; f < family.size() ; f++) - | ~~^~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 100 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 373 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 975 | for (int k=0; k&)': -phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 472 | while (h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1042 | 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 'long unsigned int'} [-Wsign-compare] - 522 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 557 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 668 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 776 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 678 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 461 | for (int i=1; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 659 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 664 | 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 'long unsigned int'} [-Wsign-compare] + 729 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'void removeMissingPhenotypes(Plink&)': +helper.cpp:775:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 795 | for (int s = 0 ; s < snps.size() ; s++) + | ~~^~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 85 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 131 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::string chromosomeName(int)': +helper.cpp:952:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 959 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 966 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 973 | for (int l=0;l getChromosomeMarkerRange(Plink&, int)': +helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 989 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector getChromosomeRange(Plink&)': +helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1040 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +linear.cpp: In member function 'double LinearModel::getPValue()': +linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] + 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; + | ^~~~ genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 154 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 161 | for (int e=0;e&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': -qfam.cpp:505:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++) - | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'void checkFileExists(std::vector >)': +helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1172 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In member function 'void Plink::prettyPrintLengths()': +helper.cpp:1264:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long 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 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] + 1273 | if (locus[l]->name.length() > par::pp_maxsnp) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:489:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 489 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 497 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 193 | for (int t=0; t::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 648 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 657 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 258 | for (int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 272 | for (int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~ -input.cpp: In member function 'bool Plink::readMultiplePhenoFile()': -input.cpp:1572:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i 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 'long unsigned int'} [-Wsign-compare] + 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1391 | for (int j=0; jmissing) + | ^ +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 'long unsigned int'} [-Wsign-compare] + 91 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~ -qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] - 639 | int tc = 0; - | ^~ -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 'long unsigned int'} [-Wsign-compare] - 267 | if ( (i+j) < a.size() ) - | ~~~~~~^~~~~~~~~~ -phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::map, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1187 | if ( nh != hapmap.size() ) - | ~~~^~~~~~~~~~~~~~~~ -input.cpp:1599:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1599 | else if (tokens.size() != par::plist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); - | ~~~~~~~~~^~~~ -input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 335 | for (int k=0; k < (*f)->kid.size() ;k++) - | ~~^~~~~~~~~~~~~~~~~~ -phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1238 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 342 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 306 | for (int i=0 ; i < s.length() ; i++) - | ~~^~~~~~~~~~~~ +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 'long 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 ); + | ^~ +haploCC.cpp: In member function 'void HaploPhase::haplotypicCC(std::map&, int, bool)': +haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 48 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ genepi.cpp:506:17: warning: unused variable 'n12' [-Wunused-variable] 506 | int n12 = n1 + n2; | ^~~ genepi.cpp:507:17: warning: unused variable 'ne' [-Wunused-variable] 507 | int ne = n1 < n2 ? n1 : n2; | ^~ -helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] - 323 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 350 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -phase.cpp:1280:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1280 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 173 | for (int s=0; ssex ) ) + | ~~^~~~~~~~~~~~~~ +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 'long 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 'long unsigned int'} [-Wsign-compare] 1025 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1033 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1792 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1299 | for (int z=0; z 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 'long unsigned int'} [-Wsign-compare] - 747 | for (int i=0; i&, int, bool)': -haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 48 | for (int z = 0 ; z < hap1[i].size(); z++) +haploCC.cpp:79:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 79 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ +haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 93 | if ( ! ( haploid || X && person->sex ) ) + | ~~^~~~~~~~~~~~~~ genepi.cpp:1043:17: warning: unused variable 'n12' [-Wunused-variable] 1043 | int n12 = n1 + n2; | ^~~ @@ -1420,106 +1041,116 @@ genepi.cpp:1064:17: warning: unused variable 'nind' [-Wunused-variable] 1064 | int nind = calcGENEPIMeanVariance(pSNP, | ^~~~ -haploCC.cpp:62:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 62 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ -haploCC.cpp:79:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 79 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 93 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ genepi.cpp: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 461 | for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 469 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 474 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 492 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 504 | for (int c=0; c&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) - | ~~^~~~~~~~~~~~~~ -input.cpp:2200:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) +tinput.cpp:261:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | 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 'long unsigned int'} [-Wsign-compare] - 2225 | for(int l=0; l < locus.size(); l++) +tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': +genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 1067 | if ( (!par::silent ) && c==c2 || c==np) + | ~~~~~~~~~~~~~~~~^~~~~~~~ +tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 309 | for (int i=0; i::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +qfam.cpp: In function 'void scoreBetween(Plink&, int)': +qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 82 | for (int k=0; k < (*f)->kid.size() ;k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 258 | for (int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~ +trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 272 | for (int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::pruneLD()': +genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 89 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 97 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +trio.cpp:335:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 335 | for (int k=0; k < (*f)->kid.size() ;k++) + | ~~^~~~~~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); | ^ -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 'long unsigned int'} [-Wsign-compare] - 272 | for (int z=1; z<=qt.size(); z++) - | ~^~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 342 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] + 1189 | int win_end = win_start + par::prune_ld_win; + | ^~~~~~~ +trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 350 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': +qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 267 | for (int i=0; i < family.size(); i++) + | ~~^~~~~~~~~~~~~~~ +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 'long 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 'long unsigned int'} [-Wsign-compare] + 132 | for (int f=0; f::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 234 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1829 | for (int z=0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1843 | for (int z=0; z < new_pp.size(); z++) - | ~~^~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 659 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 664 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) @@ -1533,29 +1164,284 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 315 | for (int f = 0 ; f < family.size() ; f++) + | ~~^~~~~~~~~~~~~~~ +trio.cpp: In member function 'void Plink::checkMendel()': +trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 469 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 474 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 492 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 504 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.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; + | ^ +tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 415 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 146 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2455 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2462 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2491 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2510 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2530 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2549 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2568 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2587 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2606 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 86 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 89 | for (int k=0; k&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': +qfam.cpp:505:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 522 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 871 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 557 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 668 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 882 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 776 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 648 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 657 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 895 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 936 | for (int f=0;f >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 80 | for ( int i = 4; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 105 | for (int i=0;i::size_type' {aka 'long 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); + | ^~~ +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 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 1038 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1048 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2671 | for (int j=1; j 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 'long unsigned int'} [-Wsign-compare] + 747 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 373 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2722 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 126 | 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::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; + | ^~~~ +binput.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 678 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ 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; | ^~~ -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 'long unsigned int'} [-Wsign-compare] - 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 145 | for (int k=0; k&)': -phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1888 | for (int z = 0; z < h1.size(); z++) - | ~~^~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 520 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 526 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1236 | for ( int k=0; kpm->kids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1245 | for ( int k=0; kpp->kids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +output.cpp:553:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 553 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 357 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 390 | for (int l=0; l > 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 'long unsigned int'} [-Wsign-compare] - 729 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 871 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 775 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 409 | for (int l=0;l&, matrix_t&, boolmatrix_t&, bool)': -helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 795 | for (int s = 0 ; s < snps.size() ; s++) - | ~~^~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 417 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 199 | for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 882 | for (int f=0; f&, std::vector&)': -perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int j=0;j< P.pS->snpset[l].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2756 | for (int j=1; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 333 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 377 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1187 | if ( nh != hapmap.size() ) + | ~~~^~~~~~~~~~~~~~~~ +merge.cpp:403:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 403 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 440 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 895 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 936 | for (int f=0;f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1238 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 426 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1280 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1299 | for (int z=0; z, Individual*>&)': +helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] + 2959 | if ( input.size() != P.nl_all ) + | ~~~~~~~~~~~~~^~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 272 | for (int z=1; z<=qt.size(); z++) + | ~^~~~~~~~~~~ +merge.cpp:722:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 722 | if ( i > include.size()) + | ~~^~~~~~~~~~~~~~~~ +merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 733 | if ( gn != 2 * include.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~~ +merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 784 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 830 | for (int i=0;i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 959 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 966 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 973 | for (int l=0;l getChromosomeMarkerRange(Plink&, int)': -helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 1040 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 842 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) + | ~~^~~~~~~~~~~~~~ +bmerge.cpp:549:11: warning: variable 'indn' set but not used [-Wunused-but-set-variable] + 549 | int indn = isample->second; + | ^~~~ +prephap.cpp: In member function 'void HaploPhase::readTagFile()': +prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 226 | if (len != tokens.size() - offset ) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 697 | while (s Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': +mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1249 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1829 | for (int z=0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 283 | for ( int i = allele ; i < tokens.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ +phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1843 | for (int z=0; z < new_pp.size(); z++) + | ~~^~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::keep2SetsForGenome()': +output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] + 788 | int n_removed = deleteIndividuals(del); + | ^~~~~~~~~ +helper.cpp: In function 'std::map, std::set > readRange(std::string)': +helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] + 3097 | set * s; + | ^ +phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': +phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1888 | for (int z = 0; z < h1.size(); z++) + | ~~^~~~~~~~~~~ +bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] + 692 | CSNP * snp; + | ^~~ +bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 839 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 871 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 883 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] + 416 | if ( tokens[index].size() != len ) + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ +prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 420 | if ( index == tokens.size() - 1 ) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~~~~~~~ cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 452 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for (int i=0;isecond; - | ^~~~ cluster.cpp:626:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +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; + | ^ cluster.cpp:651:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 651 | for (int i=0;i >)': -helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1172 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 697 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 943 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:784:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 784 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j::size_type' {aka 'long 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 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] - 1273 | if (locus[l]->name.length() > par::pp_maxsnp) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] - 692 | CSNP * snp; - | ^~~ -bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 839 | for (int i=0; i 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 'long unsigned int'} [-Wsign-compare] - 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 871 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1391 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 883 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 470 | for (int s=0;s > msqrt(std::vector >&)': +stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] + 906 | const double eps = 1e-12; + | ^~~ +prephap.cpp: In member function 'void HaploPhase::makeSlidingWindow(std::string)': +prephap.cpp:533:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 533 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 1038 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1048 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2200 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': -mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1249 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i::size_type' {aka 'long 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 'long 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 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 1531 | for (int i = 0; i < v.size(); i++) + | ~~^~~~~~~~~~ cluster.cpp:919:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2322 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 954 | for (int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::setTable()': -output.cpp:2367:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2367 | for (int i=0; i < setname.size();i++) - | ~~^~~~~~~~~~~~~~~~ cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1041:40: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2380 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1049 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1050 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1060:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1060 | for (int j1=0; j1::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2409 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1236 | for ( int k=0; kpm->kids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1245 | for ( int k=0; kpp->kids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from plink.cpp:40: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1203 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 93 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i&)': -helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] - 2204 | int i = 0; - | ^ -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 'long unsigned int'} [-Wsign-compare] - 333 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 377 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2455 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2462 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2491 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2510 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2530 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2549 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 395 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2568 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2587 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2606 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 226 | if (len != tokens.size() - offset ) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -merge.cpp:403:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 403 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 426 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | for ( int i = allele ; i < tokens.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -merge.cpp:722:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 722 | if ( i > include.size()) - | ~~^~~~~~~~~~~~~~~~ -merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 733 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 784 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 830 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 842 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] - 416 | if ( tokens[index].size() != len ) - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ -prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 420 | if ( index == tokens.size() - 1 ) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -helper.cpp:2671:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2671 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2722 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 470 | for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 533 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 560 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2756 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i, Individual*>&)': -helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} and 'int' [-Wsign-compare] - 2959 | if ( input.size() != P.nl_all ) - | ~~~~~~~~~~~~~^~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2366 | for (int l=0; l, std::set > readRange(std::string)': -helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] - 3097 | set * s; - | ^ -In file included from helper.h:24, - from assoc.cpp:24: +poo.cpp:195:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 293 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 328 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 187 | for (int i=0; i::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 273 | for (int j=0;j< P.pS->snpset[l].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::outputSetFile()': +output.cpp:2200:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 516 | if ( i == include.size() ) + | ~~^~~~~~~~~~~~~~~~~ +input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 579 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2322 | for (int j=0; j >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 2380 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int i=0; iprofileSNPs.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 'long unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2409 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2412 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 741 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2058,24 +1887,179 @@ assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 788 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ +input.cpp: In member function 'bool Plink::readClusterFile(bool)': +input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 787 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 821 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 897 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 927 | for ( int i=2; i >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1043 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1064 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1208 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1232 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 1261 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 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 ; | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp -legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': -legacy.cpp:206:65: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] - 206 | << (double)( locus[start]->bp - locus[last]->bp ) / 1000.0 - | ^ -legacy.cpp:35:7: note: 'last' was declared here - 35 | int last; - | ^~~~ -In file included from helper.h:24, - from homozyg.cpp:23: +input.cpp:1519:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1572 | for (int i=0; i >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1792 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 2225 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2471 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2366 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long 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 'long 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 'long 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 'long 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ 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); @@ -2104,67 +2088,6 @@ helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -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 'long unsigned int'} [-Wsign-compare] - 673 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 722 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 756 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 773 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 861 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': -homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1134 | if ( thispool->segs.size() >= par::pool_size_min ) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1178 | if ( thispool->segs.size() >= par::pool_size_min ) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1331 | for (int i=0; i< (*pA)->segs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1437 | for (int i=0; i < (*pA)->group.size() ; i++) - | ~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1441 | if ( (*pA)->match[i].size() >= maxlist ) - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1461 | for (int i=0; i < (*pA)->group.size() ; i++) - | ~~^~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp -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; -tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] - 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; - | ~~~^~~~~~~~~~~~~~~~~ -tdt.cpp:460:10: note: 'zt' was declared here - 460 | double zt; - | ^~ -In file included from model.cpp:17: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from glm.cpp:25: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.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) { @@ -2178,6 +2101,74 @@ linear.cpp:75:14: note: 'irow' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.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 'long 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 'long unsigned int'} [-Wsign-compare] + 368 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 377 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 381 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 384 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 390 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 415 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 424 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 460 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 461 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 462 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 467 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 480 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; | ~~~~~~^~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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"); @@ -2211,25 +2214,37 @@ dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void Model::setMissing(std::vector&)': +model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 132 | if ( include.size() != P->n ) + | ~~~~~~~~~~~~~~~^~~~~~~ dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 354 | for (int i=0; i< par::parameter_list.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 367 | for ( int i = 0 ; i < X.size() ; i++) + | ~~^~~~~~~~~~ +model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'bool Model::checkVIF()': +model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] + 613 | double maxVIF = 0; + | ^~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2257,37 +2272,18 @@ segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i&)': -model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 132 | if ( include.size() != P->n ) - | ~~~~~~~~~~~~~~~^~~~~~~ -model.cpp: In member function 'void Model::buildDesignMatrix()': -model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 354 | for (int i=0; i< par::parameter_list.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 367 | for ( int i = 0 ; i < X.size() ; i++) - | ~~^~~~~~~~~~ -model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'bool Model::checkVIF()': -model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] - 613 | double maxVIF = 0; - | ^~~~~~ -segment.cpp: In member function 'void Plink::indivSegmentSummary()': -segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] - 1855 | indivPair p = ic->first; - | ^ In file included from helper.h:24, - from glm.cpp:19: + 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +segment.cpp: In member function 'void Plink::indivSegmentSummary()': +segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] + 1855 | indivPair p = ic->first; + | ^ In file included from helper.h:24, - from logistic.cpp:20: + from glm.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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -2333,14 +2329,45 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ -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 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 673 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 722 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 756 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 773 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 861 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': +homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1134 | if ( thispool->segs.size() >= par::pool_size_min ) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1178 | if ( thispool->segs.size() >= par::pool_size_min ) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1331 | for (int i=0; i< (*pA)->segs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1437 | for (int i=0; i < (*pA)->group.size() ; i++) + | ~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1441 | if ( (*pA)->match[i].size() >= maxlist ) + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1461 | for (int i=0; i < (*pA)->group.size() ; i++) + | ~~^~~~~~~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 423 | for (int c=0; cbp - locus[last]->bp ) / 1000.0 + | ^ +legacy.cpp:35:7: note: 'last' was declared here + 35 | int last; + | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:11: warning: control reaches end of non-void function [-Wreturn-type] 849 | error("Internal problem with QFAM model specification"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp -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; - | ^~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp 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 'long unsigned int'} [-Wsign-compare] 493 | for ( int k = 0 ; k < i->second.size(); k++) @@ -2416,30 +2437,120 @@ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from proxy.cpp:24: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? 15 | #define __HAPPHASE_H__ -In file included from pdriver.cpp:18: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from haploQTL.cpp:25: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ +In file included from helper.h:24, + 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 'long 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 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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."); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:267:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 267 | prterr(2, "All elements of TABLE must be positive."); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 272 | prterr(3, "All elements of TABLE are zero.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 273 | "PRT and PRE are set to missing values."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': +fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 448 | prterr(1, "NROW must be less than or equal to LDTABL."); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 450 | prterr(4, "NCOL must be at least 2"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:449:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 449 | if (*ncol <= 1) + | ^~ +fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 453 | for (i = 1; i <= *ldkey << 1; ++i) { + | ^~~ +fisher.cpp:501:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 501 | prterr(2, "All elements of TABLE must be positive."); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 508 | prterr(3, "All elements of TABLE are zero.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 509 | "PRT and PRE are set to missing values."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 559 | prterr(5, "The hash table key cannot be computed because " + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 560 | "the largest key\n" + | ~~~~~~~~~~~~~~~~~~~ + 561 | "is larger than the largest representable int.\n" + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 562 | "The algorithm cannot proceed.\n" + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 563 | "Reduce the workspace size, or use `exact = FALSE'."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 750 | prterr(6, "LDKEY is too small for this problem.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 751 | "Try increasing the size of the workspace."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from pdriver.cpp:18: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': +fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 1538 | prterr(6, "LDKEY is too small for this problem.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1539 | "Try increasing the size of the workspace."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:1554:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 1554 | prterr(7, "LDSTP is too small for this problem.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1555 | "Try increasing the size of the workspace."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 1596 | prterr(7, "LDSTP is too small for this problem.\n" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1597 | "Try increasing the size of the workspace."); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp 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 'long unsigned int'} [-Wsign-compare] 76 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 86 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ @@ -2470,47 +2581,24 @@ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp -assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': -assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] - 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) - | ^~ -assoc.cpp:1019:14: note: 'pvalue' was declared here - 1019 | double pvalue; - | ^~~~~~ -In file included from haplohelper.cpp:25: +In file included from haploQTL.cpp:25: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? 15 | #define __HAPPHASE_H__ -In file included from haplohelper.cpp:27: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from haplohelper.cpp:28: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from lookup.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 'long 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: +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from proxy.cpp:21: +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -2519,28 +2607,21 @@ linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 206 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 272 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 289 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from haplohelper.cpp:25: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from haplohelper.cpp:27: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from haplohelper.cpp:28: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 128 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 206 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 272 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 289 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from haplowindow.cpp:27: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from haplowindow.cpp:28: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from haplowindow.cpp:30: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ +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; + | ^~~~~~ 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >&, 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; + | ^~~~~~~~~~~ proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:314:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 314 | for (int i=1; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp -pdriver.cpp: In member function 'void Plink::proxyWrapper()': -pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] - 266 | int similar = 0; - | ^~~~~~~ proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2691,6 +2730,21 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ -In file included from haplowindow.cpp:27: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from haplowindow.cpp:28: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from haplowindow.cpp:30: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ -In file included from genogroup.cpp:24: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from genogroup.cpp:28: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from genogroup.cpp:29: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp -In file included from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - 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++/15/bits/ostream.h:232:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { 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++/15/bits/ostream.h:232:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { 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++/15/bits/ostream.h:232:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { 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++/15/bits/ostream.h:232:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { 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; - | ^~~~~~~~~ -glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] - 610 | double pvalue = chiprobP(chisq,df); - | ~~~~~~~~^~~~~~~~~~ -glm.cpp:556:15: note: 'df' was declared here - 556 | int df; - | ^~ -In file included from nonfounderphasing.cpp:27: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from nonfounderphasing.cpp:28: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from nonfounderphasing.cpp:29: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ -output.cpp: In member function 'void Plink::display_indivReport()': -output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 69 | << setw(6) << genotype(*this,i1,l) << "\n"; - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:46:7: note: 'i1' was declared here - 46 | int i1; - | ^~ -In file included from 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 134 | for (int l=0; l < actual_map.size(); l++) | ~~^~~~~~~~~~~~~~~~~~~ +pdriver.cpp: In member function 'void Plink::proxyWrapper()': +pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] + 266 | int similar = 0; + | ^~~~~~~ haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 297 | for (int h=0; h::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1225 | for (int z = 0; z < hap1[p1].size(); z++) @@ -2883,7 +2840,6 @@ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) | ~~~^~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++) | ~~~^~~~~~~~~~~~~~~~~ @@ -2901,71 +2857,21 @@ haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from clumpld.cpp:21: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from genoerr.cpp:27: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from genoerr.cpp:28: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from genoerr.cpp:29: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp -In file included from em.cpp:27: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from em.cpp:28: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from em.cpp:29: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::prunePhase(int, double)': haplowindow.cpp:558:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) @@ -2998,21 +2899,12 @@ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ -In file included from impute.cpp:27: -genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __GENOGROUP_H_ -genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? - 15 | #define __GENOGROUP_H__ -In file included from impute.cpp:28: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ -In file included from impute.cpp:29: -haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] - 13 | #ifndef __HAPWINDOW_H_ -haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? - 14 | #define __HAPWINDOW_H__ +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; + | ^~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 683 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 872 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 949 | for (int z = 0; z < hap1[i].size(); z++) @@ -3050,21 +2934,112 @@ haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long 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; +In file included from genogroup.cpp:24: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from genogroup.cpp:28: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from genogroup.cpp:29: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ +In file included from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + 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++/15/bits/ostream.h:232:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { 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++/15/bits/ostream.h:232:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { 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++/15/bits/ostream.h:232:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { 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++/15/bits/ostream.h:232:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { 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; + | ^~~~~~~~~ +In file included from clumpld.cpp:21: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from nonfounderphasing.cpp:27: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from nonfounderphasing.cpp:28: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from nonfounderphasing.cpp:29: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:27: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from genoerr.cpp:28: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from genoerr.cpp:29: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ +In file included from em.cpp:27: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from em.cpp:28: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from em.cpp:29: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ 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) @@ -3072,6 +3047,11 @@ merge.cpp:943:8: note: 'write' was declared here 943 | bool write; | ^~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: @@ -3079,11 +3059,24 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from genoerr.cpp:24: +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp +In file included from nonfounderphasing.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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~ clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 201 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 189 | for( int a = 0; a < posshap1.size(); a++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for( int b = 0; b < posshap2.size(); b++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 225 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 358 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 368 | for (int i = 0; i < sp.size(); i++) + | ~~^~~~~~~~~~~ +clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 480 | if( l1 < P->locus.size()-1 ) + | ~~~^~~~~~~~~~~~~~~~~~~ +clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 520 | for (int f=1; f<=filename.size(); f++) + | ~^~~~~~~~~~~~~~~~~ +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 'long 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; + | ^~~~ +clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int f=1; f<=filename.size(); f++) + | ~^~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~~ +In file included from impute.cpp:27: +genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __GENOGROUP_H_ +genogroup.h:15: note: '__GENOGROUP_H__' is defined here; did you mean '__GENOGROUP_H_'? + 15 | #define __GENOGROUP_H__ +In file included from impute.cpp:28: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +In file included from impute.cpp:29: +haplowindow.h:13: warning: header guard '__HAPWINDOW_H_' followed by '#define' of a different macro [-Wheader-guard] + 13 | #ifndef __HAPWINDOW_H_ +haplowindow.h:14: note: '__HAPWINDOW_H__' is defined here; did you mean '__HAPWINDOW_H_'? + 14 | #define __HAPWINDOW_H__ +clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1097 | if( j < grouped_snps.size()-1) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 368 | for (int i = 0; i < sp.size(); i++) - | ~~^~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 480 | if( l1 < P->locus.size()-1 ) - | ~~~^~~~~~~~~~~~~~~~~~~ em.cpp: In member function 'void HaploPhase::performEM_original()': em.cpp:89:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 132 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ em.cpp:162:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 162 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 166 | for (int z=0; z >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 611 | for (int f=1; f<=filename.size(); f++) - | ~^~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1097 | if( j < grouped_snps.size()-1) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 105 | for (int z=0; z::size_type' {aka 'long 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 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] - 313 | for (int s=0; s < g.size(); s++) - | ~~^~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h:14: warning: header guard '__GENOGROUP_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __GENOGROUP_H_ @@ -3251,6 +3236,10 @@ In file included from metaem.cpp:28: phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] 14 | #ifndef __HAPPHASE_H_ +genoerr.cpp: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': +genoerr.cpp:157:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 189 | for( int a = 0; a < posshap1.size(); a++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 190 | for( int b = 0; b < posshap2.size(); b++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 225 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 328 | for (int z2=0; z2::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 358 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 105 | for (int z=0; z::size_type' {aka 'long 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 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 313 | for (int s=0; s < g.size(); s++) + | ~~^~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] - 304 | bool OLD_clist = par::clist; - | ^~~~~~~~~ -profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] - 350 | double statistic = valid ? model->getStatistic() : 0; - | ^~~~~~~~~ -profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] - 351 | double pvalue = pval[ pval.size()-1 ]; - | ^~~~~~ -profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] - 352 | double beta = b[ b.size()-1 ]; - | ^~~~ -profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 390 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 402 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 421 | if ( qcnt == qlabel.size() ) - | ~~~~~^~~~~~~~~~~~~~~~ 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 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i&, 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 'long 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 'long unsigned int'} [-Wsign-compare] - 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from gvar.cpp:15: +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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -3437,28 +3403,55 @@ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -In file included from greport.cpp:20: +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; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] + 304 | bool OLD_clist = par::clist; + | ^~~~~~~~~ +profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] + 350 | double statistic = valid ? model->getStatistic() : 0; + | ^~~~~~~~~ +profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] + 351 | double pvalue = pval[ pval.size()-1 ]; + | ^~~~~~ +profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] + 352 | double beta = b[ b.size()-1 ]; + | ^~~~ +profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 390 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 402 | for (int s=0; s >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -cnv.cpp: In member function 'void Plink::readCNVList()': -cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] - 247 | int p1,p2; - | ^~ -cnv.cpp:247:18: warning: unused variable 'p2' [-Wunused-variable] - 247 | int p1,p2; - | ^~ -cnv.cpp:332:19: warning: unused variable 'p1' [-Wunused-variable] - 332 | int p1,p2; - | ^~ -cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] - 332 | int p1,p2; - | ^~ -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 'long unsigned int'} [-Wsign-compare] - 125 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 635 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 679 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 192 | for (int l=0; l >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 147 | if ( tokens.size() <= chr_column || - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 148 | tokens.size() <= bp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 156 | if ( tokens.size() <= pval_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 169 | if ( tokens.size() <= snp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs_QT()': simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1211 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 247 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 298 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 381 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 395 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ simul.cpp:1358:30: warning: unused variable 'cumU' [-Wunused-variable] 1358 | double cumA = 0, cumU = 0; | ^~~~ -gvar.cpp:403:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 403 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 240 | for (int l=0; l< ari->second.size(); l+=2) - | ~^~~~~~~~~~~~~~~~~~~~ -cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] - 678 | map::iterator is = idescription.find(*ir); - | ^~ -cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 815 | for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 825 | for (int s2=s1+1; s2second; - | ^~ -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 'long unsigned int'} [-Wsign-compare] - 549 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 553 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 556 | for (int i=0; i::iterator i2 = isection.begin(); - | ^~ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'bool RCount::addSNP(int)': +elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] + 374 | double wt; + | ^~ whap.cpp:393:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 393 | for (int g=0; g::size_type' {aka 'long unsigned int'} [-Wsign-compare] 456 | for (int h=0; h&, int, int, int)': -cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] - 1749 | int cnt = 0; - | ^~~ whap.cpp:508:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3610,30 +3520,16 @@ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ -cnv.cpp: In member function 'void Plink::positionPermuteSegments()': -cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2013 | for (int c = 0 ; c < scaffold.size(); c++) - | ~~^~~~~~~~~~~~~~~~~ -cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': -cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] - 2098 | noCovar == true; - | ~~~~~~~~^~~~~~~ -cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] - 2202 | indivPair p = ic->first; - | ^ -cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] - 2288 | double statistic = valid ? model->getStatistic() : 0; - | ^~~~~~~~~ -cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] - 2289 | double pvalue = pval[ pval.size()-1 ]; - | ^~~~~~ -cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] - 2290 | double beta = b[ b.size()-1 ]; - | ^~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 962 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ whap.cpp:986:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 986 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1162 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1197 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp -In file included from idhelp.cpp:18: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from idhelp.cpp:19: +In file included from helper.h:24, + from gvar.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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from blox.cpp:23: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ +cnv.cpp: In member function 'void Plink::readCNVList()': +cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] + 247 | int p1,p2; + | ^~ +cnv.cpp:247:18: warning: unused variable 'p2' [-Wunused-variable] + 247 | int p1,p2; + | ^~ +cnv.cpp:332:19: warning: unused variable 'p1' [-Wunused-variable] + 332 | int p1,p2; + | ^~ +cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] + 332 | int p1,p2; + | ^~ +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 'long unsigned int'} [-Wsign-compare] + 125 | for (int l=0; l::iterator is = idescription.find(*ir); + | ^~ +cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 815 | for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 825 | for (int s2=s1+1; s2::iterator i2 = isection.begin(); + | ^~ +gvar.cpp:192:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 192 | for (int l=0; l::iterator il = segmentLength.find(t); + | ^~ +gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 247 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 298 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 381 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int i=0; i::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] + 549 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 553 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 556 | for (int i=0; i&, int, int, int)': +cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] + 1749 | int cnt = 0; + | ^~~ +cnv.cpp: In member function 'void Plink::positionPermuteSegments()': +cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2013 | for (int c = 0 ; c < scaffold.size(); c++) + | ~~^~~~~~~~~~~~~~~~~ +cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': +cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] + 2098 | noCovar == true; + | ~~~~~~~~^~~~~~~ +cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] + 2202 | indivPair p = ic->first; + | ^ +cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] + 2288 | double statistic = valid ? model->getStatistic() : 0; + | ^~~~~~~~~ +cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] + 2289 | double pvalue = pval[ pval.size()-1 ]; + | ^~~~~~ +cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] + 2290 | double beta = b[ b.size()-1 ]; + | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.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 'long unsigned int'} [-Wsign-compare] + 78 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 147 | if ( tokens.size() <= chr_column || + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 148 | tokens.size() <= bp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 156 | if ( tokens.size() <= pval_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 169 | if ( tokens.size() <= snp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from helper.h:24, - from qualscores.cpp:24: + from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -3724,11 +3726,89 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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; + | ^~~ +In file included from helper.h:24, + from qualscores.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +cfamily.cpp: In function 'int mCount(Individual*, Individual*)': +cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 205 | for (int i = 0 ; i < inds.size() ; i++) + | ~~^~~~~~~~~~~~~ +cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~ +cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 237 | for (int i = 0 ; i < inds.size() ; i++) + | ~~^~~~~~~~~~~~~ +cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': +cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 263 | for (int i = 0 ; i < inds.size() ; i++) + | ~~^~~~~~~~~~~~~ +cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~ +cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 288 | for (int i = 0 ; i < inds.size() ; i++) + | ~~^~~~~~~~~~~~~ +In file included from hapglm.cpp:25: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ +qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': +qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] + 122 | long int nfound = 0; + | ^~~~~~ In file included from 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp +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 'long unsigned int'} [-Wsign-compare] + 80 | for (int i=0; i >::size_type' {aka 'long 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 'long 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 'long unsigned int'} [-Wsign-compare] + 196 | for (int i=0; i < snpset[j].size(); i++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp +In file included from idhelp.cpp:18: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from blox.cpp:23: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) @@ -3736,10 +3816,10 @@ idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 63 | for (int i=0; i vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1405:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] + 1405 | int maxI; + | ^~~~ 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 'long unsigned int'} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) @@ -3763,33 +3843,14 @@ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] 214 | vector & jo = jointOrder[j]; | ^~ -In file included from helper.h:24, - from flip.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 80 | for (int i=0; i IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ -setscreen.cpp:110:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long 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 'long unsigned int'} [-Wsign-compare] - 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) - | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 502 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ -setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int i=0; i < snpset[j].size(); i++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 510 | if ( p < tokens.size() ) | ~~^~~~~~~~~~~~~~~ @@ -3847,26 +3908,6 @@ idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -cfamily.cpp: In function 'int mCount(Individual*, Individual*)': -cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 205 | for (int i = 0 ; i < inds.size() ; i++) - | ~~^~~~~~~~~~~~~ -cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~ -cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 237 | for (int i = 0 ; i < inds.size() ; i++) - | ~~^~~~~~~~~~~~~ -cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': -cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 263 | for (int i = 0 ; i < inds.size() ; i++) - | ~~^~~~~~~~~~~~~ -cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~ -cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 288 | for (int i = 0 ; i < inds.size() ; i++) - | ~~^~~~~~~~~~~~~ idhelp.cpp:888:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3912,7 +3953,6 @@ idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -4016,11 +4056,15 @@ idhelp.cpp:2034:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2034 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp +In file included from helper.h:24, + from lookup2.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -4033,6 +4077,12 @@ idhelp.cpp:2201:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2201 | for (int k = 0 ; k < thisLine.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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2229 | for ( int g = 0 ; g < idgroup.size(); g++ ) @@ -4040,18 +4090,6 @@ idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp -In file included from helper.h:24, - from lookup2.cpp:18: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from dosage.cpp:23: -phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] - 14 | #ifndef __HAPPHASE_H_ -phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? - 15 | #define __HAPPHASE_H__ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) @@ -4065,36 +4103,32 @@ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1405:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] - 1405 | int maxI; - | ^~~~ +proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] + 422 | int ref; + | ^~~ In file included from helper.h:24, - from hapglm.cpp:20: + 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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] - 422 | int ref; - | ^~~ +In file included from dosage.cpp:23: +phase.h:14: warning: header guard '__HAPPHASE_H_' followed by '#define' of a different macro [-Wheader-guard] + 14 | #ifndef __HAPPHASE_H_ +phase.h:15: note: '__HAPPHASE_H__' is defined here; did you mean '__HAPPHASE_H_'? + 15 | #define __HAPPHASE_H__ 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 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from helper.h:24, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from tag.cpp:24: +In file included from blox.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 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -4132,21 +4166,32 @@ blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp +In file included from dosage.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 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +dosage.cpp: In member function 'void Plink::processDosageFile()': +dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 110 | for ( int q = 0 ; q < qthresh.size() ; q++) + | ~~^~~~~~~~~~~~~~~~ annot.cpp:149:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': -metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] - 47 | int bp; - | ^~ -metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] - 44 | string a1; - | ^~ -metaanal.cpp:61:3: warning: when initialized here [-Wreorder] - 61 | Alleles(string name, int chr, int bp, string a1, string a2) - | ^~~~~~~ -metaanal.cpp: In member function 'void Plink::metaAnalysis()': -metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 159 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 182 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 213 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 300 | if ( tokens.size() != fsize ) - | ~~~~~~~~~~~~~~^~~~~~~~ -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 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 680 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 110 | for ( int q = 0 ; q < qthresh.size() ; q++) - | ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 513 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) +dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 989 | for (int q=0; qgetStatistic() : 0; + | ^~~~~~~~~ +dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1252 | if ( o->second != dosageFilename_all.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1310 | if ( ++qq == qthresh.size() ) + | ~~~~~^~~~~~~~~~~~~~~~~ +dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] + 190 | int geno_field = a2_field + skip2 + 1; + | ^~~~~~~~~~ In file included from 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] @@ -4263,9 +4266,6 @@ 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 */ | ^~~~~~~~~~~~~~ -dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': +metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] + 47 | int bp; + | ^~ +metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] + 44 | string a1; + | ^~ +metaanal.cpp:61:3: warning: when initialized here [-Wreorder] + 61 | Alleles(string name, int chr, int bp, string a1, string a2) + | ^~~~~~~ +metaanal.cpp: In member function 'void Plink::metaAnalysis()': +metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 159 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 182 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 213 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 300 | if ( tokens.size() != fsize ) + | ~~~~~~~~~~~~~~^~~~~~~~ +metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] + 253 | int pval_column = -1; + | ^~~~~~~~~~~ +metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 680 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -dosage.cpp:1170:18: warning: unused variable 'statistic' [-Wunused-variable] - 1170 | double statistic = valid ? model->getStatistic() : 0; - | ^~~~~~~~~ -dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1252 | if ( o->second != dosageFilename_all.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1310 | if ( ++qq == qthresh.size() ) - | ~~~~~^~~~~~~~~~~~~~~~~ -dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] - 190 | int geno_field = a2_field + skip2 + 1; - | ^~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp 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] @@ -4346,30 +4406,6 @@ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ -blox.cpp:510:10: warning: 'pA1' may be used uninitialized [-Wmaybe-uninitialized] - 510 | double D = pA1 - (pA*p1); - | ^ -blox.cpp:489:10: note: 'pA1' was declared here - 489 | double pA1,pA2,pB1,pB2; - | ^~~ -blox.cpp:503:10: warning: 'pA2' may be used uninitialized [-Wmaybe-uninitialized] - 503 | double pA = pA1 + pA2; - | ^~ -blox.cpp:489:14: note: 'pA2' was declared here - 489 | double pA1,pA2,pB1,pB2; - | ^~~ -blox.cpp:505:10: warning: 'pB1' may be used uninitialized [-Wmaybe-uninitialized] - 505 | double p1 = pA1 + pB1; - | ^~ -blox.cpp:489:18: note: 'pB1' was declared here - 489 | double pA1,pA2,pB1,pB2; - | ^~~ -blox.cpp:565:51: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] - 565 | double loglike1 = unknownDH * log( pA1*pB2 + pB1*pA2 ); - | ~~~^~~~ -blox.cpp:489:22: note: 'pB2' was declared here - 489 | double pA1,pA2,pB1,pB2; - | ^~~ input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) @@ -4390,7 +4426,7 @@ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' make[1]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' - dh_auto_test +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs @@ -4430,12 +4466,14 @@ 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/3252757/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3252757/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/3901677 and its subdirectories -I: Current time: Sun Dec 20 15:04:48 -12 2026 -I: pbuilder-time-stamp: 1797822288 +I: removing directory /srv/workspace/pbuilder/3252757 and its subdirectories +I: Current time: Tue Nov 18 10:44:04 +14 2025 +I: pbuilder-time-stamp: 1763412244