Diff of the two buildlogs: -- --- b1/build.log 2025-03-01 22:31:41.207607967 +0000 +++ b2/build.log 2025-03-01 22:48:45.217540302 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 3 16:52:59 -12 2026 -I: pbuilder-time-stamp: 1775278379 +I: Current time: Sun Mar 2 12:31:44 +14 2025 +I: pbuilder-time-stamp: 1740868304 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3130882/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3572130/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 Mar 1 22:32 /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/3572130/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3572130/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='unstable' - 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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='31d2d01d98b349d78a46d9bd5a4c9f9c' - 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='3130882' - PS1='# ' - PS2='> ' + INVOCATION_ID=dea089b4b598492baa774607ec13883d + 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=3572130 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.EgcFLfbt/pbuilderrc_3xLB --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EgcFLfbt/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='111' - 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.EgcFLfbt/pbuilderrc_Y0G6 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EgcFLfbt/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=111 + 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 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3130882/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3572130/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: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 21.5 MB in 3s (8047 kB/s) +Fetched 21.5 MB in 2s (13.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19780 files and directories currently installed.) @@ -280,7 +312,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/3572130/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3572130/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -292,7 +328,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j42 clean + make -j20 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' @@ -307,7 +343,7 @@ 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 -j20 "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 @@ -330,192 +366,16 @@ 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 prephap.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 phase.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 tdt.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 sharing.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 genepi.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 perm.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 mh.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 genedrop.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 gxe.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.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 multiple.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 haploCC.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 poo.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 webcheck.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 qfam.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 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 -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 -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 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 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 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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from perm.h:17, - from genedrop.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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 mishap.cpp:17: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 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 binput.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 252 | for (int i=0; i&, 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++) - | ~^~~~~~~~~~~~~~~~~~~~ -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] - 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 sets.cpp:24: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp: In member function 'void Set::sizeSets()': -sets.cpp:37:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 37 | for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 52 | for(int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 59 | else if (par::set_min > snpset[i].size() ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -sets.cpp:62:48: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 62 | if (par::set_max==-1 || par::set_max > snpset[i].size() ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 99 | for(int i=0;i::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] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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] - 351 | while (c<7 && s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 176 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -binput.cpp:398:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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()) - | ~~^~~~~~~~~~~~~~~~ -mishap.cpp: In member function 'void Plink::performMisHapTests()': -mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -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() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -sets.cpp: In member function 'void Set::dropNotSet(Plink&)': -sets.cpp:216:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 216 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j < snpset[i].size(); j++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -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&, std::vector&, std::vector >&)': +stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] + 458 | int m,l,iter,i,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(); + | ^ +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; + | ^~~ +stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': +stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) + | ~~^~~~~~~~~~ +In file included from tinput.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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] + 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] + 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] 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::display_twolocus()': +output.cpp:402:28: warning: variable 'loc1' set but not used [-Wunused-but-set-variable] + 402 | vector::iterator loc1 = locus.begin()+m1; + | ^~~~ 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++) | ~~^~~~~~~~~~~~~~ +output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] + 403 | vector::iterator loc2 = locus.begin()+m2; + | ^~~~ 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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 236 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 237 | for (int j=0; j < snpset[i].size(); j++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp: In member function 'void Set::makeLDSets()': -sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 317 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 323 | for (int j=0; j < snpset[i].size(); j++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 329 | for (int j=0; j < snpset[i].size(); j++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp:332:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 332 | for (int k=j+1; k < snpset[i].size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 591 | if ( c > sample.size()) | ~~^~~~~~~~~~~~~~~ -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] 603 | if ( gn != 2 * sample.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 395 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 412 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 403 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 413 | for (int j=0; j < snpset[i].size(); j++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from epi.cpp:23: +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] + 526 | 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -merge.cpp:426:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 426 | 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 gxe.cpp:20: +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); + | ^~~~~~~~~ +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 hotel.cpp:23: +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; - | ^~~~ +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() ) + | ~~~^~~~~~~~~~~~~~~~~~~~~ +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] + 695 | for (int i=0; i >::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::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::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 722 | if ( i > include.size()) - | ~~^~~~~~~~~~~~~~~~ -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] - 632 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 733 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -sets.cpp:642:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 642 | 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] - 643 | for (int j=0;j::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] - 703 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | 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] - 784 | 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -merge.cpp:830:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] + 2322 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 787 | 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 553 | 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from plink.cpp:28: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp:713:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 713 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int i=0; i >::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] + 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'} 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] - 591 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ 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] - 611 | 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 >&)': +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] + 76 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ input.cpp:961:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 961 | else if ( ccount != tokens.size() ) | ~~~~~~~^~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~ 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) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~ 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] 1064 | 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 ); - | ^~ 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'} and 'int' [-Wsign-compare] 1256 | if (tokens.size() < 2+par::mult_covar) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -filters.cpp:739:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++ ) - | ~~^~~~~~~~~~~~~~~ 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] - 82 | for (int k=0; k < (*f)->kid.size() ;k++) - | ~~^~~~~~~~~~~~~~~~~~ -sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': -sets.cpp:905:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1335 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for ( int k=0; k<(*f)->kid.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: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++) - | ~^~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from helper.cpp:24: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~ -sets.cpp:975:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 975 | for (int k=0; kperson[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++) - | ~~^~~~~~~~~~~~~~~~~ -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] - 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 210 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -epi.cpp: In member function 'void Plink::calcEpistasis()': -epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 234 | for (int f=0; f::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] - 252 | for (int i=0; imissing) - | ^ -poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': -poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 93 | for (int f=0; f >::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::fromPriorLog(std::string)': +helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 193 | for (int t=0; t > 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+" "); + | ~~~~~~~~~^~~~ +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 ) + | ~~^~~~~~~~~~~~~~~ +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'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +filters.cpp: In member function 'void Plink::filterSNPs()': +filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 91 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~ -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] - 327 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from genepi.cpp:24: +In file included from helper.h:24, + from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -multiple.cpp:131:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 131 | 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] + 461 | for (int i=1; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int i=0; iprofileSNPs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~ +filters.cpp:273:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 273 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 741 | for (int j=0; jselectedSNPs[l].size(); j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 785 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +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'} 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] + 788 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ +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] + 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'} [-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 > 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] + 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++) + | ~~^~~~~~~~~~~~~ +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; + | ^~~~~~ +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&, 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 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] + 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++ ) + | ~~^~~~~~~~~~~~~~~ +input.cpp:2172:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) + | ~~^~~~~~~~~~~~~~ +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] + 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;ifreq * ( 1 - locus[l]->freq ); + | ^~ +input.cpp:2419:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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'} 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) + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': +input.cpp:2471:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2471 | 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; j Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] + 1536 | int best = 0 ; + | ^~~~ +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++) + | ~^~~~~~~~~~~ +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] + 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] + 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -1082,384 +984,83 @@ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] 848 | double e21 = E21*S; | ^~~ -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++) - | ~~^~~~~~~~~~~~~~~ -epi.cpp:438:26: warning: unused variable 'zero' [-Wunused-variable] - 438 | double zero = 0; - | ^~~~ -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&, std::vector&, std::vector >&)': -stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] - 458 | int m,l,iter,i,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) - | ~~~~~~~~~~~~~~~~^~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~ -filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] - 368 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -legacy.cpp:377:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] + 372 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1143 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 415 | 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] - 424 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ filters.cpp: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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': -multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 295 | for (int i=0;i&)': -phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 472 | while (h::size_type' {aka '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 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] - 372 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 226 | if (len != tokens.size() - offset ) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -phase.cpp: In member function 'void HaploPhase::performAlternEM()': -phase.cpp:678:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 678 | for (int z=0; z 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&, 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++ ) - | ~~^~~~~~~~~~~~~~~ -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] - 467 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 668 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 480 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 776 | for (int f=0; f::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] - 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++) - | ~~^~~~~~~~~~ -filters.cpp: In member function 'void Plink::thinSNPs()': -filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] - 1277 | int x = 0; - | ^ -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++) - | ~^~~~~~~~~~~~~~~ -prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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 ) - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ +plink.cpp: In function 'int main(int, char**)': +plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 763 | par::make_founders && + | ~~~~~~~~~~~~~~~~~~~^~ + 764 | !par::built_families) + | ~~~~~~~~~~~~~~~~~~~~ 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] - 420 | if ( index == tokens.size() - 1 ) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 342 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ cluster.cpp:511:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 350 | for ( int k=0; k<(*f)->kid.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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; 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] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ 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, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1187 | if ( nh != hapmap.size() ) - | ~~~^~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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'} [-Wsign-compare] - 1238 | 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] - 1280 | for (int z=0; z::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::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 470 | for (int s=0;s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 469 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 533 | for (int i=0; i::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] - 560 | 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 >&)': -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] - 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++) - | ~^~~~~~~~~~ +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] 919 | for (int k=0;k&)': -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++) - | ~^~~~~~~~~~ -input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] 954 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 955 | 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++) - | ~~^~~~~~~~~~~~~~ cluster.cpp:975:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 975 | 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] - 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) - | ~~^~~~~~~~~~~~~~ +helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': +helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] + 2204 | int i = 0; + | ^ cluster.cpp:1050:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1050 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1061 | for (int j2=0; j2::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] 1107 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1163 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 871 | for (int f=0; f::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++) - | ~~^~~~~~~~~~~~~~~ -trio.cpp:882:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 882 | for (int f=0; f::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 >&, 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] 1204 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2587 | for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1228 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1229 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2606 | for (int i=0; i&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1254 | 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] - 895 | for (int c=0; c 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] + 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1661 | if ( col_length != tokens.size() ) + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1664 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2106 | 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] + 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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] + 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] + 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] + 2756 | for (int j=1; j, Individual*>&)': +helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 ) + | ~~~~~~~~~~~~~^~~~~~~~~~~ +epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] + 701 | int c=0; + | ^ +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 ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ +In file included from phase.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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::set > readRange(std::string)': +helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] + 3097 | set * s; + | ^ +In file included from prephap.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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; + | ^~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 tdt.cpp +In file included from phase.cpp:28: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 373 | for (int i=0; i&)': +phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 472 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 678 | for (int z=0; z >::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() ) + | ~~~^~~~~~~~~~~~~~~~ +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] + 1280 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1299 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 226 | if (len != tokens.size() - offset ) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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++ ) + | ~~^~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~ +phase.cpp:1575:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) + | ~~^~~~~~~~~~~~~~ +phase.cpp: In member function 'void HaploPhase::prunePhase(int)': +phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~ +prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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 ) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~ -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] + 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] + 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++) + | ~^~~~~~~~~~~~~~~ +prephap.cpp:560:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 335 | for (int k=0; k < (*f)->kid.size() ;k++) + | ~~^~~~~~~~~~~~~~~~~~ +trio.cpp:342:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 342 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 350 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +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] + 871 | 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] + 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] - 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | 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); + | ^~~ +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 > 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+" "); - | ~~~~~~~~~^~~~ +trio.cpp: In member function 'void Plink::makeMissingParents()': +trio.cpp:1236:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp: In member function 'std::string CArgs::value(std::string)': +helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] + 218 | error("Missing an argument for "+s); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +helper.cpp: In member function 'int CArgs::value_int(std::string)': +helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] + 231 | error("Missing an argument for "+s); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': +helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] + 243 | error("Missing an argument for "+s); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +helper.cpp: In member function 'double CArgs::value_double(std::string)': +helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] + 255 | error("Missing an argument for "+s); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +helper.cpp: In function 'int getInt(std::string, std::string)': +helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] + 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': +helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] + 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +helper.cpp: In function 'double getDouble(std::string, std::string)': +helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] + 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from tdt.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 genepi.cpp +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] + 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 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~~~~~ +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] + 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': +sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~~~~ +genepi.cpp: In function 'double C(int, double, double)': +genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] + 78 | } + | ^ +genepi.cpp: In function 'long double pillai(int, int, int, double)': +genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] + 169 | } + | ^ +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 >&, 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 >&, 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&, 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; + | ^~~~~~~~~~~~~~~~~ +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 genedrop.cpp +tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] + 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; + | ~~~^~~~~~~~~~~~~~~~~ +tdt.cpp:460:10: note: 'zt' was declared here + 460 | double zt; + | ^~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > 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 ) - | ~~^~~~~~~~~~~~~~~ -cluster.cpp: In member function 'void Plink::groupGenome()': -cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 37 | for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 52 | for(int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 59 | else if (par::set_min > snpset[i].size() ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +sets.cpp:62:48: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 62 | if (par::set_max==-1 || par::set_max > snpset[i].size() ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +sets.cpp: In member function 'void Set::pruneSets(Plink&)': +sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 99 | for(int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 129 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 176 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 216 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j < snpset[i].size(); j++) + | ~~^~~~~~~~~~~~~~~~~~ +sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 236 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 237 | for (int j=0; j < snpset[i].size(); j++) + | ~~^~~~~~~~~~~~~~~~~~ +sets.cpp: In member function 'void Set::makeLDSets()': +sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 317 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 323 | for (int j=0; j < snpset[i].size(); j++) + | ~~^~~~~~~~~~~~~~~~~~ +sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 329 | for (int j=0; j < snpset[i].size(); j++) + | ~~^~~~~~~~~~~~~~~~~~ +sets.cpp:332:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 332 | for (int k=j+1; k < snpset[i].size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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] - 309 | if (i == s.length()-1) t += s[i]; - | ~~^~~~~~~~~~~~~~~ -cluster.cpp:1661:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1661 | if ( col_length != tokens.size() ) - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -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] - 1664 | 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); - | ^~~ +sets.cpp:370:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 370 | for (int j=0; j < snpset[i].size(); j++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 631 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 632 | for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 642 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 643 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 703 | 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'} [-Wsign-compare] + 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 975 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1042 | 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 perm.h:17, + from perm.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::display_indivReport()': +output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] + 69 | << setw(6) << genotype(*this,i1,l) << "\n"; + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:46:7: note: 'i1' was declared here + 46 | int i1; + | ^~ +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 gxe.cpp +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&, 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++) + | ~^~~~~~~~~~~~~~~~~~~~ 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] - 252 | for (int i=0; i::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 >&, 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&, 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: 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] - 395 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': +assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] + 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) + | ^~ +assoc.cpp:1019:14: note: 'pvalue' was declared here + 1019 | double pvalue; + | ^~~~~~ +mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': +mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 747 | 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::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/iostream:41, + from assoc.cpp:14: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: +/usr/include/c++/14/ostream: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++/14/ostream: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++/14/ostream: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++/14/ostream: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 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 hotel.cpp +In file included from merge.cpp:22: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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] - 1048 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 403 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 426 | for (int i=0; i::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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': +hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 77 | if (!sample[i]->missing) + | ^ +hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 173 | for (int s=0; s >::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] + 131 | 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 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 qfam.cpp +In file included from haploCC.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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&, 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: 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; - | ^~~~~~~~~~~~~~~~~ haploCC.cpp:62:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 62 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ @@ -1738,231 +1958,186 @@ haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 93 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -assoc.cpp:741:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 741 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 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] - 785 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -trio.cpp: In member function 'void Plink::makeMissingParents()': -trio.cpp:1236:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 > 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 >&, 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; + | ^~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); | ^ -helper.cpp:729:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 729 | for (int h=0; h::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++) - | ~~^~~~~~~~~~~~~ -mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': -mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1249 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ -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() ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ haploCC.cpp:357:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 357 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -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] 375 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ -helper.cpp: In function 'int getMarkerNumber(Plink&, std::string)': -helper.cpp:966:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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;lsex ) ) | ~~^~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector getChromosomeMarkerRange(Plink&, int)': -helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 >)': -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'} 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) - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1389 | 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] - 2200 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -output.cpp:2322:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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] - 2409 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2412 | for (int l=0; l Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] - 1536 | int best = 0 ; - | ^~~~ -plink.cpp: In function 'int main(int, char**)': -plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 763 | par::make_founders && - | ~~~~~~~~~~~~~~~~~~~^~ - 764 | !par::built_families) - | ~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': -helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] - 2204 | int i = 0; - | ^ -helper.cpp: In member function 'void Plink::filterOnCovariate()': -helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] + 93 | for (int f=0; f > >::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++) + | ~~^~~~~~~~~~~~~~~~~~ +webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': +webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 117 | 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] + 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] - 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2671 | for (int j=1; j >::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++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~ +qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, 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++) + | ~~^~~~~~~~~~~~~~~~~~ +qfam.cpp:648:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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, int>&)': +merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] + 1103 | if (write) + | ^~ +merge.cpp:943:8: note: 'write' was declared here + 943 | bool write; + | ^~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 +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 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 mishap.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from mishap.cpp:20: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~~~~ +mishap.cpp: In member function 'void Plink::performMisHapTests()': +mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -helper.cpp: In member function 'void Plink::attribFilterInd()': -helper.cpp:2722:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2722 | 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] - 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] + 50 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 409 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 673 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ bmerge.cpp:417:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 417 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2756 | for (int j=1; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ bmerge.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 440 | 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 ) - | ~~~~~~~~~~~~~^~~~~~~~~~~ -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 -helper.cpp: In function 'std::map, std::set > readRange(std::string)': -helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] - 3097 | set * s; - | ^ +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++) + | ~~^~~~~~~~~~~~~~ bmerge.cpp:549:11: warning: variable 'indn' set but not used [-Wunused-but-set-variable] 549 | int indn = isample->second; | ^~~~ @@ -2016,35 +2194,12 @@ bmerge.cpp:883:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 883 | 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++) - | ~~^~~~~~~~~~~~~~ -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; - | ^~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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 ) @@ -2064,110 +2219,61 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~ +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 *xn)) goto S160; - | ~~~~~~~~~~~~^~~~~~~~~~~ -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) { - | ^~ -linear.cpp:75:9: note: 'icol' was declared here - 75 | int i,icol,irow,j,k,l,ll; - | ^~~~ -linear.cpp:96:5: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] - 96 | if (irow != icol) { - | ^~ -linear.cpp:75:14: note: 'irow' was declared here - 75 | int i,icol,irow,j,k,l,ll; - | ^~~~ -dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': -dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; - | ~~~~~~^~~~~~~~~~~~~~ -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; - | ~~~~~~^~~~~~~~~~~~~ -dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; - | ~~~~~~^~~~~~~~~~~~~~ -dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; - | ~~~~~~^~~~~~~~~~~~~~ -dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] - 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; - | ^~~ -dcdflib.cpp: In function 'double dlanor(double*)': -dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dcdflib.cpp: In function 'double dstrem(double*)': -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"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 helper.h:24, - from segment.cpp:20: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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:15: +In file included from model.cpp:17: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) @@ -2176,6 +2282,7 @@ segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) | ^~ +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 segment.cpp:875:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 875 | SIBS << setw(10) << original[l] << " " | ^~~~ @@ -2195,21 +2302,47 @@ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] 950 | int c=0; | ^ +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 ) + | ~~~~~~~~~~~~~~~^~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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::summaryIBD()': 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; ifirst; | ^ 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 elf.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp -In file included from model.cpp:17: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i&)': -model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka '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; - | ^~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 *xn)) goto S160; + | ~~~~~~~~~~~~^~~~~~~~~~~ +dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': +dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; + | ~~~~~~^~~~~~~~~~~~~~ +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; + | ~~~~~~^~~~~~~~~~~~~ +dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; + | ~~~~~~^~~~~~~~~~~~~~ +dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; + | ~~~~~~^~~~~~~~~~~~~~ +dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] + 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; + | ^~~ +dcdflib.cpp: In function 'double dlanor(double*)': +dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dcdflib.cpp: In function 'double dstrem(double*)': +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"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 helper.h:24, 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++) | ~~^~~~~~~~~~~~~~~~~~ -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 linput.cpp In file included from glm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2314,14 +2451,66 @@ model.cpp:849:10: 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 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 +legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': +legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] + 203 | << start - last - 1 << " "; + | ~~~~~~^~~~~~ +legacy.cpp:35:7: note: 'last' was declared here + 35 | int last; + | ^~~~ +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) { + | ^~ +linear.cpp:75:9: note: 'icol' was declared here + 75 | int i,icol,irow,j,k,l,ll; + | ^~~~ +linear.cpp:96:5: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] + 96 | if (irow != icol) { + | ^~ +linear.cpp:75:14: note: 'irow' was declared here + 75 | int i,icol,irow,j,k,l,ll; + | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': +elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 609 | for (int l=0; l< original.size(); l++) + | ~^~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': +elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] + 654 | const double pthresh = 0.01; + | ^~~~~~~ +elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] + 655 | bool one_sided = true; + | ^~~~~~~~~ +elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] + 707 | int srange_cnt = 0; + | ^~~~~~~~~~ +elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] + 708 | bool inRange = false; + | ^~~~~~~ +elf.cpp: In member function 'void Plink::displayRareRange()': +elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 895 | for (int i = 0 ; i < tokens.size() ; i++) + | ~~^~~~~~~~~~~~~~~ +elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 939 | if ( tokens.size() != ncol ) + | ~~~~~~~~~~~~~~^~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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] @@ -2361,88 +2550,6 @@ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~ -elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': -elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 609 | for (int l=0; l< original.size(); l++) - | ~^~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': -elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] - 654 | const double pthresh = 0.01; - | ^~~~~~~ -elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] - 655 | bool one_sided = true; - | ^~~~~~~~~ -elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] - 707 | int srange_cnt = 0; - | ^~~~~~~~~~ -elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] - 708 | bool inRange = false; - | ^~~~~~~ -elf.cpp: In member function 'void Plink::displayRareRange()': -elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 895 | for (int i = 0 ; i < tokens.size() ; i++) - | ~~^~~~~~~~~~~~~~~ -elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 939 | if ( tokens.size() != ncol ) - | ~~~~~~~~~~~~~~^~~~~~~ -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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -linput.cpp: In member function 'void Plink::readDataLongFormat()': -linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 68 | for (int l=0; l< locus.size(); l++) - | ~^~~~~~~~~~~~~~ -linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 128 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 136 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | for (int l=0; l< locus.size(); l++) - | ~^~~~~~~~~~~~~~ -linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 164 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 200 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 209 | for (int i=0; i > socketConnection(Plink*, std::string, int, std::string)': -sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] - 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request - | ^~~~~~~ -sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] - 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response - | ^~~~~~ -sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] - 81 | unsigned int i; // Loop counter - | ^ -sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] - 119 | int echoStringLen = 100; - | ^~~~~~~~~~~~~ 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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2529,13 +2623,76 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 +linput.cpp: In member function 'void Plink::readDataLongFormat()': +linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 68 | for (int l=0; l< locus.size(); l++) + | ~^~~~~~~~~~~~~~ +linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 128 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 136 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 146 | for (int l=0; l< locus.size(); l++) + | ~^~~~~~~~~~~~~~ +linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 164 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 200 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 209 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': +sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] + 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request + | ^~~~~~~ +sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] + 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response + | ^~~~~~ +sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] + 81 | unsigned int i; // Loop counter + | ^ +sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] + 119 | int echoStringLen = 100; + | ^~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readData()': +input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] + 91 | if ( feof(PED) ) + | ~~~~^~~~~ +input.cpp:60:10: note: 'PED' was declared here + 60 | FILE * PED; + | ^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 +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 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++) | ~~^~~~~~~~~~~~~~~~~~ -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 +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 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] 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 haploQTL.cpp:24: +In file included from proxy.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++) @@ -2578,39 +2728,21 @@ 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&, int, bool)': -haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 83 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 145 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ pdriver.cpp: In member function 'void Plink::proxyWrapper()': pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] 266 | int similar = 0; | ^~~~~~~ -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 proxy.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 clumpld.cpp In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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: 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 ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +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 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from haploQTL.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, int, bool)': +haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 83 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ -merge.cpp:943:8: note: 'write' was declared here - 943 | bool write; - | ^~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1401 | for (int c1 = 0; c1 < collection.size() ; c1++ ) | ~~~^~~~~~~~~~~~~~~~~~~ -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 proxy.cpp:1448:19: warning: unused variable 't1' [-Wunused-variable] 1448 | int t1=0; | ^~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ -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 haplowindow.cpp:23: +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++) | ~~^~~~~~~~~~~~~~~~~~ +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 +elf.cpp: In member function 'bool RCount::addSNP(int)': +elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] + 374 | double wt; + | ^~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2670,7 +2806,6 @@ haplohelper.cpp:104:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 134 | for (int l=0; l < actual_map.size(); l++) | ~~^~~~~~~~~~~~~~~~~~~ @@ -2693,6 +2828,11 @@ haplohelper.cpp:487:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 487 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ +In file included from haplowindow.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 655 | for (int z=0; z::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ -In file included from haplowindow.cpp:27: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++) @@ -2790,10 +2877,6 @@ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] 1250 | int j=0; | ^ -haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': -haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1419 | for( int z = 0; z < pp[i].size(); z++ ) @@ -2801,19 +2884,32 @@ haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1477 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ -haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': -haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from genogroup.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from haplowindow.cpp:27: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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] + 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': +haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) @@ -2843,6 +2939,27 @@ haplowindow.cpp:872:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 872 | for (int z=0; z::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: +/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bmerge.cpp: In member function 'void Plink::mergeBinaryData()': +bmerge.cpp:682:16: note: 'indn' was declared here + 682 | int indn; + | ^~~~ haplowindow.cpp: In member function 'void HaploWindow::reportPhase()': haplowindow.cpp:949:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 949 | for (int z = 0; z < hap1[i].size(); z++) @@ -2850,6 +2967,25 @@ 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 nonfounderphasing.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] @@ -2864,27 +3000,37 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | 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; - | ^~~~~~~~~~~ -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 -In file included from nonfounderphasing.cpp:24: +In file included from nonfounderphasing.cpp:28: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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; + | ^~~~~~~~~ +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 helper.h:24, + from clumpld.h:21, + from clumpld.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 clumpld.h:21, - from clumpld.cpp:20: +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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from nonfounderphasing.cpp:27: +In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from nonfounderphasing.cpp:28: +In file included from em.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: -/usr/include/c++/14/ostream: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++/14/ostream: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++/14/ostream: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++/14/ostream: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; - | ^~~~~~~~~ +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] + 97 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 106 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 128 | 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] + 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] + 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] @@ -2962,40 +3102,12 @@ clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from genoerr.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] 201 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.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 nlist.cpp -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; - | ^~~~ -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; - | ^~ -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 genoerr.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3014,10 +3126,6 @@ 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++) | ~~^~~~~~~~~~~~~~~~~ -clumpld.cpp: In member function 'void clump_LD::clump()': -clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 368 | for (int i = 0; i < sp.size(); i++) - | ~~^~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~ @@ -3030,11 +3138,13 @@ 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 ) | ~~~^~~~~~~~~~~~~~~~~~~ -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 simul.cpp 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++) | ~^~~~~~~~~~~~~~~~~ @@ -3044,54 +3154,13 @@ 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 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 -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++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from em.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from em.cpp:28: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 97 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 106 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 128 | 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] - 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] @@ -3101,11 +3170,7 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) - | ~~^~~~~~~~~~~~~~~~~~ +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 simul.cpp In file included from impute.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3119,22 +3184,12 @@ impute.cpp:105:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 105 | 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] 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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++) @@ -3142,16 +3197,70 @@ 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: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 metaem.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~~~~ metaem.cpp: In member function 'void HaploPhase::enumeratePhasedWindows(int)': metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 239 | while (hgetStatistic() : 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'bool RCount::addSNP(int)': -elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] - 374 | double wt; - | ^~ +profile.cpp: In function 'void scoreRanges(int, std::vector&, 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 NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 38 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from helper.h:24, from 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 profile.cpp:23: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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 qualscores.cpp -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from bmerge.cpp:14: -In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: -/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bmerge.cpp: In member function 'void Plink::mergeBinaryData()': -bmerge.cpp:682:16: note: 'indn' was declared here - 682 | int indn; - | ^~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] 172 | double gh_11_12 = h11*h12; | ^~~~~~~~ -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 cnvqt.cpp simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1211 | for (int s=0; sgetStatistic() : 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 ]; - | ^~~~ simul.cpp:1358:30: warning: unused variable 'cumU' [-Wunused-variable] 1358 | double cumA = 0, cumU = 0; | ^~~~ -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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -profile.cpp: In function 'void scoreRanges(int, std::vector&, 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 192 | 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] - 247 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -gvar.cpp:298:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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; i >::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; hsecond; - | ^~ -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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ -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; - | ^~ whap.cpp:793:12: 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() ) | ~~~^~~~~~~~~~~~~~~~ @@ -3433,6 +3412,105 @@ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1334 | for (int l=0; l&, ChapModel&)': +whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1389 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1425 | for (int h=0; h < m.group.size(); h++) + | ~~^~~~~~~~~~~~~~~~ +whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) + | ~~~~~^~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 +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] + 192 | for (int l=0; l::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 >::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; + | ^~ +In file included from helper.h:24, + from step.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ @@ -3442,10 +3520,6 @@ cnv.cpp:825:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 825 | for (int s2=s1+1; s2&, ChapModel&)': -whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1389 | for (int l=0;l::iterator i2 = isection.begin(); | ^~ -whap.cpp: In function 'void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)': -whap.cpp:1425:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1425 | for (int h=0; h < m.group.size(); h++) - | ~~^~~~~~~~~~~~~~~~ -whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) - | ~~~~~^~~~~~~~~~~~~~~~~~~ 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 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 setscreen.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++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ @@ -3477,42 +3548,10 @@ cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; | ^~~ -In file included from helper.h:24, - from step.cpp:18: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 ]; - | ^~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ 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 || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ @@ -3531,42 +3570,54 @@ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ -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; - | ^~~~ +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 idhelp.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 tag.cpp In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 tag.cpp -In file included from helper.h:24, - from cnvqt.cpp:22: +In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 In file included from helper.h:24, - from qualscores.cpp: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++) | ~~^~~~~~~~~~~~~~~~~~ -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 lookup2.cpp -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 cfamily.cpp:18: +proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] + 422 | int ref; + | ^~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -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 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++) @@ -3587,13 +3638,22 @@ 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++) | ~~^~~~~~~~~~~~~ +qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': +qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] + 122 | long int nfound = 0; + | ^~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp +In file included from idhelp.cpp:18: +idhelp.h: In member function 'void IDGroup::display()': +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 helper.h:24, - from tag.cpp:24: +In file included from idhelp.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -3608,27 +3668,9 @@ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~ -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] 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 -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 idhelp.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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: 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++) @@ -3636,19 +3678,6 @@ 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 163 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 203 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 280 | for (int i = 0 ; i < ids.size(); i++) - | ~~^~~~~~~~~~~~ -lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 325 | for (int t = 0 ; t < tokens.size() ; t++) - | ~~^~~~~~~~~~~~~~~ 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++) @@ -3663,11 +3692,9 @@ idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int j = 0 ; j < jointField.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 metaanal.cpp idhelp.cpp:221:26: 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 < 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 idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 296 | for ( int i = 0 ; i < mask.size() ; i++) | ~~^~~~~~~~~~~~~ @@ -3733,15 +3760,15 @@ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 794 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ -idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ @@ -3796,11 +3823,7 @@ idhelp.cpp:1128:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1128 | for ( int k = 0; k < (*i0)->values.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from hapglm.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1183 | for (int z=0; zvalues.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ @@ -3913,19 +3936,6 @@ 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++ ) | ~~^~~~~~~~~~~~~~~~~ -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; - | ^~~~~~ 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++ ) @@ -3933,6 +3943,40 @@ 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 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 +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 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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from hapglm.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 203 | for (int i = 0 ; i < ids.size(); i++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 280 | for (int i = 0 ; i < ids.size(); i++) + | ~~^~~~~~~~~~~~ +lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 325 | for (int t = 0 ; t < tokens.size() ; t++) + | ~~^~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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()': @@ -3944,13 +3988,12 @@ 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 Rconnection.cpp In file included from blox.cpp:23: 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 > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; @@ -3980,43 +4023,17 @@ blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ +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 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++) | ~~^~~~~~~~~~~~~~~~~~ -annot.cpp: In member function 'void Plink::annotateFile()': -annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 83 | 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] - 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 250 | if ( tokens.size() <= chr_column || - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 251 | tokens.size() <= bp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 260 | if ( tokens.size() <= pval_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 275 | if ( tokens.size() <= snp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] - 300 | bool include = false; - | ^~~~~~~ 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++) @@ -4038,12 +4055,7 @@ | ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) -In file included from helper.h:24, - from r.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 Rconnection.cpp 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 +annot.cpp: In member function 'void Plink::annotateFile()': +annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 250 | if ( tokens.size() <= chr_column || + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 251 | tokens.size() <= bp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 260 | if ( tokens.size() <= pval_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 275 | if ( tokens.size() <= snp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] + 300 | bool include = false; + | ^~~~~~~ In file included from Rconnection.cpp:30: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -4083,11 +4123,6 @@ 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 */ | ^~~~~~~~~~~~~~ -In file included from metaanal.cpp:21: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 567 | if (host) free(host); host=0; @@ -4095,29 +4130,11 @@ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 567 | if (host) free(host); host=0; | ^~~~ -In file included from r.cpp:29: -Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': -Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 203 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] - 422 | int ref; - | ^~~ +In file included from metaanal.cpp:21: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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; @@ -4128,10 +4145,6 @@ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] 61 | Alleles(string name, int chr, int bp, string a1, string a2) | ^~~~~~~ -r.cpp: In member function 'void Plink::Rfunc()': -r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] - 330 | int ct = data->length(); - | ^~ 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'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ +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; + | ^~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] 253 | int pval_column = -1; | ^~~~~~~~~~~ @@ -4166,6 +4203,36 @@ metaanal.cpp:680:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from r.cpp:29: +Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': +Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 203 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': +Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 206 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In member function 'char* Rstrings::stringAt(int)': +Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +r.cpp: In member function 'void Plink::Rfunc()': +r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] + 330 | int ct = data->length(); + | ^~ r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -4196,37 +4263,6 @@ 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) ) - | ~~~~^~~~~ -input.cpp:60:10: note: 'PED' was declared here - 60 | FILE * PED; - | ^~~ dosage.cpp:915:35: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] 915 | SNP[snp_code]->one[personPosition[f][i]] = s1; | ^ @@ -4280,12 +4316,14 @@ 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/3572130/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3572130/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/3130882 and its subdirectories -I: Current time: Fri Apr 3 16:54:40 -12 2026 -I: pbuilder-time-stamp: 1775278480 +I: removing directory /srv/workspace/pbuilder/3572130 and its subdirectories +I: Current time: Sun Mar 2 12:48:44 +14 2025 +I: pbuilder-time-stamp: 1740869324