Diff of the two buildlogs: -- --- b1/build.log 2025-08-27 11:16:18.182173309 +0000 +++ b2/build.log 2025-08-27 11:18:27.246330206 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 29 05:30:32 -12 2026 -I: pbuilder-time-stamp: 1790703033 +I: Current time: Thu Aug 28 01:16:21 +14 2025 +I: pbuilder-time-stamp: 1756293381 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1451901/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1353141/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 Aug 27 11:16 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1353141/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1353141/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d00f4c00e03d4de1ab4929df8230658b' - 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='1451901' - PS1='# ' - PS2='> ' + INVOCATION_ID=7951ae18f45243e5ba7f1e3ad578a6fc + 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=1353141 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.JVgVWkDD/pbuilderrc_mOKI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JVgVWkDD/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JVgVWkDD/pbuilderrc_nDhd --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JVgVWkDD/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1451901/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1353141/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.25 [937 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.1 MB in 3s (3948 kB/s) +Fetched 12.1 MB in 4s (3054 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19855 files and directories currently installed.) @@ -276,7 +308,11 @@ 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/1353141/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1353141/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 @@ -288,7 +324,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j42 clean + make -j40 clean make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' @@ -303,7 +339,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 - make -j42 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 + make -j40 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp @@ -346,248 +382,73 @@ 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 multi.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from hotel.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 304 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 357 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 372 | for (int i=0; imissing) - | ^ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -bmerge.cpp: In member function 'void Plink::mergeBinaryData()': -bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] - 90 | long int inc; - | ^~~ -bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 357 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 390 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 409 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 417 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 440 | for (int i=0; isecond; - | ^~~~ -bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 697 | while (s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] - 692 | CSNP * snp; - | ^~~ -bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 839 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 871 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 883 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 >::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] - 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 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++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~ -In file included from helper.h:24, - from assoc.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from binput.cpp:23: +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 sets.cpp:20: + 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++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~ -In file included from locus.cpp:16: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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] + 64 | 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] - 474 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int l=0; l::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] + 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) + | ~~^~~~~~~~~~~~~~~~~~~ +In file included from output.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -trio.cpp:943:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] + 218 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1048 | for (int c=0; c >::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() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ 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] - 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': -stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] - 458 | int m,l,iter,i,k; - | ^ -In file included from assoc.cpp:29: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ -assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': -assoc.cpp:395:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 395 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ -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 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~ -In file included from helper.h:24, - from cluster.cpp:23: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] - 1536 | int best = 0 ; - | ^~~~ -In file included from helper.h:24, - from webcheck.cpp:19: +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) @@ -724,11 +484,6 @@ 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++) - | ~~^~~~~~~~~~~~~~~~~~ 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] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from output.cpp:23: +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] + 357 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 390 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 409 | 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 perm.h:17, - from perm.cpp:17: +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] + 440 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -790,24 +573,117 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +merge.cpp:395:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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;lsecond; + | ^~~~ +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] 367 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 697 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 370 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] + 692 | CSNP * snp; + | ^~~ +bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 839 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 871 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ +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] + 722 | if ( i > include.size()) + | ~~^~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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::iterator loc1 = locus.begin()+m1; + | ^~~~ +In file included from helper.h:24, + from multiple.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++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] + 403 | vector::iterator loc2 = locus.begin()+m2; + | ^~~~ +merge.cpp:842:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) + | ~~^~~~~~~~~~~~~~~~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp:553:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 553 | for (int l=0; l > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 618 | 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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] 643 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from gxe.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'vector_t Set::profileTestScore()': sets.cpp:703:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 703 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +perm.cpp: In member function 'void Perm::permuteInCluster()': +perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 199 | for(int i=0; i&, std::vector&)': +perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 273 | for (int j=0;j< P.pS->snpset[l].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +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] + 304 | for (int i=0;imissing) + | ^ +multi.cpp:357:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 357 | 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] + 372 | 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 sharing.cpp:19: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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] - 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] - 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 95 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 123 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 132 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 155 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 163 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 198 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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&, std::vector&, std::vector >&)': +stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] + 458 | int m,l,iter,i,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] + 273 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 91 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~ +filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] + 249 | double freq; + | ^~~~ +filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] + 250 | int nm; + | ^~ +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); + | ^~~~~~~~~ +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; + | ^~~ 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; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i::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++) + | ~~^~~~~~~~~~~~~~ +mds.cpp: In member function 'void Plink::generateMDS()': +mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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] + 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++ ) + | ~~^~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~ +linear.cpp: In member function 'virtual void LinearModel::pruneY()': +linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 50 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | 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++) + | ~^~~~~~~~~~~~~~~ +tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 93 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +tinput.cpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 146 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +epi.cpp:154:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 335 | for (int k=0; k < (*f)->kid.size() ;k++) + | ~~^~~~~~~~~~~~~~~~~~ +epi.cpp:161:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~ +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] + 350 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ +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] + 195 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +linear.cpp: In member function 'double LinearModel::getPValue()': +linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] + 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; + | ^~~~ +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++) + | ~^~~~~~~~~~~~~~~~~~~~~ +filters.cpp:1143:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1143 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1165 | for ( int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | if ( c > sample.size()) + | ~~^~~~~~~~~~~~~~~ +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] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ +trio.cpp:504:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 504 | for (int c=0; c 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++) | ~~^~~~~~~~~~~~~~~~~~ +poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] + 239 | double zt; + | ^~ +filters.cpp: In member function 'void Plink::thinSNPs()': +filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] + 1277 | int x = 0; + | ^ +epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] + 701 | int c=0; + | ^ +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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ -In file included from haploCC.cpp:24: +trio.cpp:871:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': -homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 673 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 722 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 756 | for (int i=0; i < plist.size(); i++) - | ~~^~~~~~~~~~~~~~ -In file included from tdt.cpp:23: +In file included from helper.h:24, + from assoc.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~ -In file included from genepi.cpp:24: +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++) | ~~^~~~~~~~~~~~~~~~~~ +trio.cpp:943:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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); + | ^~~ 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] 786 | for (int j=0;j >::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 ) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1178 | if ( thispool->segs.size() >= par::pool_size_min ) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -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] - 1331 | for (int i=0; i< (*pA)->segs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~ -filters.cpp:155:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] - 1437 | for (int i=0; i < (*pA)->group.size() ; i++) - | ~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1441 | if ( (*pA)->match[i].size() >= maxlist ) - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1461 | for (int i=0; i < (*pA)->group.size() ; i++) - | ~~^~~~~~~~~~~~~~~~~~~~~ +trio.cpp: In member function 'void Plink::pseudoCaseControl()': +trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1038 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1048 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j::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++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +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'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from genome.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp:1049:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1049 | 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] 1050 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1163 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 271 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -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] 1169 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | 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] + 2200 | 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] - 252 | 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] 1276 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In function 'bool pairable_cluster(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1290 | 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] - 102 | for (int l=0; l >::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] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 226 | if (len != tokens.size() - offset ) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::writeSetFile()': +output.cpp:2409:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2409 | 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] + 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] + 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 283 | for ( int i = allele ; i < tokens.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ +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; + | ^~~~~~ +phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': +phase.cpp:373:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 373 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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 'void HaploPhase::enumerateHaplotypes(std::vector&)': +phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 472 | while (h >::size_type' {aka '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 ); + | ^~ +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::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 470 | for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 533 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1187 | if ( nh != hapmap.size() ) + | ~~~^~~~~~~~~~~~~~~~ +genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': +genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] + 843 | double e10 = E10*S; + | ^~~ +genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] + 844 | double e20 = E20*S; + | ^~~ +genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] + 848 | double e21 = E21*S; + | ^~~ +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] + 252 | 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] + 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) + | ~~^~~~~~~~~~~~~~ +assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': +assoc.cpp:395:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int i=0; iprofileSNPs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~ +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] + 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++) + | ~~^~~~~~~~~~~~~~~ +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++) @@ -1126,9 +1415,16 @@ 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++) | ~~^~~~~~~~~~~~~~~~ -filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] - 250 | int nm; - | ^~ +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++) + | ~~^~~~~~~~~~~ +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 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haploCC.cpp:62:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 62 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ @@ -1138,36 +1434,21 @@ haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 93 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -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] - 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] - 591 | 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++) + | ~^~~~~~~~~~~~~~~~~~~~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -filters.cpp:611:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 591 | if ( c > sample.size()) - | ~~^~~~~~~~~~~~~~~ -tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) @@ -1181,160 +1462,6 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': -homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] - 2155 | homozygWindows[l] == 0; -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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -output.cpp:86:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] - 333 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 739 | for ( int l = 0 ; l < locus.size() ; l++ ) - | ~~^~~~~~~~~~~~~~ -merge.cpp:377:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 377 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 762 | for ( int i = 0 ; i < sample.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -merge.cpp:395:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] - 81 | for (int i=0; iperson.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -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] - 234 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 327 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -merge.cpp:722:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 722 | if ( i > include.size()) - | ~~^~~~~~~~~~~~~~~~ -merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 733 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -perm.cpp: In member function 'void Perm::setOriginalRanking(vector_t&)': -perm.cpp:187:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 199 | for(int i=0; i&, std::vector&)': -perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int j=0;j< P.pS->snpset[l].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -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] - 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++) - | ~^~~~~~~~~~~~~~~~~~~~~ -merge.cpp:842:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 842 | 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] - 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] - 1143 | for (int l=0; l::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++) - | ~~^~~~~~~~~~~~~~~~~~ -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] 516 | if ( i == include.size() ) @@ -1345,6 +1472,7 @@ 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() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ +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 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] 631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -filters.cpp: In member function 'void Plink::thinSNPs()': -filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] - 1277 | int x = 0; - | ^ -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 | } - | ^ -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; - | ^~~~ -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] 695 | 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] - 497 | 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] - 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++) - | ~~^~~~~~~~~~~~~~~~~~ -genepi.cpp:506:17: warning: unused variable 'n12' [-Wunused-variable] - 506 | int n12 = n1 + n2; - | ^~~ -genepi.cpp:507:17: warning: unused variable 'ne' [-Wunused-variable] - 507 | int ne = n1 < n2 ? n1 : n2; - | ^~ -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 ); - | ^~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -genepi.cpp: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': -genepi.cpp:1025:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1025 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1033 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -legacy.cpp:395:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 395 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] - 226 | if (len != tokens.size() - offset ) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 787 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | for ( int i = allele ; i < tokens.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -linear.cpp: In member function 'double LinearModel::getPValue()': -linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] - 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; - | ^~~~ -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] - 480 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.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() ) - | ~~~~~~^~~~~~~~~~~~~~~ +helper.cpp: In function 'std::string display(std::vector >&)': +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++) + | ~^~~~~~~~~~ +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++) + | ~^~~~~~~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] + 1536 | int best = 0 ; + | ^~~~ input.cpp:817:25: warning: comparison of integer expressions of different signedness: 'std::vector >::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'} 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 ) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -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] 897 | for (int i=0; i > >::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++) - | ~^~~~~~~~~~~~~~~~~~~~~ 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'} and 'int' [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -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] 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1064 | for (int i=0; i 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] - 470 | for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1208 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1256 | if (tokens.size() < 2+par::mult_covar) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -prephap.cpp: In member function 'void HaploPhase::makeSlidingWindow(std::string)': -prephap.cpp:533:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 533 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1261 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 560 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1335 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': -mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1249 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | for (int e=0;e >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -epi.cpp:154:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] - 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] - 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++) - | ~~^~~~~~~~~~~~~~~~~~ -input.cpp:1519:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1599 | else if (tokens.size() != par::plist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} 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); - | ^~~~ -input.cpp:1745:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1792 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >&)': -helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 58 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | 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&, 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] - 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] - 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 90 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -input.cpp:2210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 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: In member function 'void Plink::readFamFile(std::string)': -input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i&, 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] - 373 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 131 | 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] + 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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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 >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'std::vector > CArgs::value(std::string, int)': helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) @@ -1839,27 +1622,21 @@ 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, 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] - 196 | for (int k=0; k::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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': helper.cpp:461:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 461 | for (int i=1; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'void summaryBasics(Plink&)': helper.cpp:595:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) - | ~~^~~~~~~~~~~~~~ helper.cpp: In function 'double genotypingRate(Plink&, int)': helper.cpp:659:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 659 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 664 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c > 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] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~ +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'} 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] 952 | if ( c < 0 || c >= par::chr_code.size() ) @@ -1923,10 +1706,6 @@ 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&)': -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++) - | ~~^~~~~~~~~~~ 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'} and 'int' [-Wsign-compare] 1264 | if (sample[i]->fid.length() > par::pp_maxfid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp:1745:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1745 | for (int c=0; c::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:1764:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c 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] - 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] + 1792 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2225 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +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]; + | ^~~~~~ +input.cpp: In member function 'void Plink::readFamFile(std::string)': +input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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:2453:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i >::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] + 2471 | for (int i=0; i::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 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; | ^ +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++) + | ~^~~~~~~~~~~~~~~~~ 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] + 97 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ helper.cpp:2462:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2462 | for (int j=0; j::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] 2606 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 267 | for (int i=0; i < family.size(); i++) + | ~~^~~~~~~~~~~~~~~ +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++) + | ~^~~~~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'void Plink::attribFilterSNP()': helper.cpp:2638:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 315 | for (int f = 0 ; f < family.size() ; f++) + | ~~^~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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 >::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&, 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2756 | for (int j=1; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2935 | for (int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ -plink.cpp: In member function 'void Plink::cleanUp()': -plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2366 | for (int l=0; l, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; | ^ +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 helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] 3324 | int last = -1; @@ -2062,20 +1941,226 @@ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] 3329 | int nextChromosome; | ^~~~~~~~~~~~~~ +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) + | ~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~~~~~~~~~~ +plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i::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++) + | ~~^~~~~~~~~~~~~~~~~~ +legacy.cpp: In member function 'void Plink::calcRegression(int)': +legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 368 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 377 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 381 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 384 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 390 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 395 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 415 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 424 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 460 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 461 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 462 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 467 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 480 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': +homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 673 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ 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 +homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 722 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 756 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 773 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 861 | for (int i=0; i < plist.size(); i++) + | ~~^~~~~~~~~~~~~~ +homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': +homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1134 | if ( thispool->segs.size() >= par::pool_size_min ) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1178 | if ( thispool->segs.size() >= par::pool_size_min ) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1331 | for (int i=0; i< (*pA)->segs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1437 | for (int i=0; i < (*pA)->group.size() ; i++) + | ~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1441 | if ( (*pA)->match[i].size() >= maxlist ) + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1461 | for (int i=0; i < (*pA)->group.size() ; i++) + | ~~^~~~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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 -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; - | ^~~~ -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 +homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': +homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] + 2155 | homozygWindows[l] == 0; +tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] + 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; + | ~~~^~~~~~~~~~~~~~~~~ +tdt.cpp:460:10: note: 'zt' was declared here + 460 | double zt; + | ^~ +In file included from model.cpp:17: +phase.h: 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 *xn)) goto S160; @@ -2084,6 +2169,7 @@ dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; | ~~~~~~^~~~~~~~~~~~~~ +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 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"); @@ -2113,44 +2199,6 @@ 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp -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++) - | ~~^~~~~~~~~~~~~~~~~~ -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 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 ) @@ -2169,66 +2217,12 @@ model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 -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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from segment.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 294 | for (int h=1; h < whap->current->group.size(); h++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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) { - | ^~ -glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 423 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~ -model.cpp: In member function 'double Model::buildQFAM(Individual*)': -model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] - 849 | error("Internal problem with QFAM model specification"); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': -dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 76 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 86 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 96 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 106 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 271 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 378 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] - 218 | bool informative = false; - | ^~~~~~~~~~~ -dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 504 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] - 151 | int totalInformative = 0; - | ^~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2303,10 +2265,18 @@ segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;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 sockets.cpp segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] 2003 | int nseg = smap.size(); @@ -2348,41 +2318,59 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ +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; + | ^~ +model.cpp: In member function 'double Model::buildQFAM(Individual*)': +model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] + 849 | error("Internal problem with QFAM model specification"); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 294 | for (int h=1; h < whap->current->group.size(); h++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 423 | for (int c=0; c >::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 -In file included from linput.cpp:25: +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++) | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2001 | prterr(40, "Out of workspace."); @@ -2462,8 +2444,6 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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 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++) @@ -2472,6 +2452,8 @@ 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++) | ~^~~~~~~~~~~~~~~~~ +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 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; @@ -2485,7 +2467,6 @@ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] 708 | bool inRange = 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 haploQTL.cpp 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++) @@ -2493,7 +2474,102 @@ 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +linput.cpp:209:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 209 | for (int i=0; i, 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; + | ^~~~~ +dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': +dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 76 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 86 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 96 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 106 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 271 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 378 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] + 218 | bool informative = false; + | ^~~~~~~~~~~ +dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 504 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] + 151 | int totalInformative = 0; + | ^~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from 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++) + | ~~^~~~~~~~~~~~~~~~~~ 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 +sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': +sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] + 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request + | ^~~~~~~ +sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] + 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response + | ^~~~~~ +sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] + 81 | unsigned int i; // Loop counter + | ^ +sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] + 119 | int echoStringLen = 100; + | ^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': @@ -2516,53 +2592,125 @@ lookup.cpp:289:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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++) | ~~^~~~~~~~~~~~~~~~~~ -sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': -sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] - 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request - | ^~~~~~~ -sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] - 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response - | ^~~~~~ -sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] - 81 | unsigned int i; // Loop counter - | ^ -sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] - 119 | int echoStringLen = 100; - | ^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp +In file included from 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 ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: 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] + 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~ pdriver.cpp: In member function 'void Plink::proxyWrapper()': pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] 266 | int similar = 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 haplowindow.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp +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++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++ ) + | ~~~^~~~~~~~~~~~~~~~~~~ +proxy.cpp:1448:19: warning: unused variable 't1' [-Wunused-variable] + 1448 | int t1=0; + | ^~ +proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] + 169 | CSNP * s = SNP[l]; + | ^ +glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] + 610 | double pvalue = chiprobP(chisq,df); + | ~~~~~~~~^~~~~~~~~~ +glm.cpp:556:15: note: 'df' was declared here + 556 | int df; + | ^~ +In file included from haploQTL.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 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++) + | ~~^~~~~~~~~~~~~~~~ +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:1307:21, + 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; + | ^~~~ +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++) + | ~~^~~~~~~~~~~~~~~~ +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 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 nonfounderphasing.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp +assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': +assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] + 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) + | ^~ +assoc.cpp:1019:14: note: 'pvalue' was declared here + 1019 | double pvalue; + | ^~~~~~ In file included from haplohelper.cpp:25: 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] @@ -2649,50 +2797,18 @@ 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++ ) | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 em.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 ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++ ) - | ~~~^~~~~~~~~~~~~~~~~~~ -proxy.cpp:1448:19: warning: unused variable 't1' [-Wunused-variable] - 1448 | int t1=0; - | ^~ -proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] - 169 | CSNP * s = SNP[l]; - | ^ 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] @@ -2720,7 +2836,6 @@ haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) @@ -2771,106 +2886,6 @@ 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 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 haploQTL.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_pairList()': -output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] - 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:11: note: 'i2' was declared here - 116 | int i1, i2; - | ^~ -output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:7: note: 'i1' was declared here - 116 | int i1, i2; - | ^~ -In file included from 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++) - | ~~^~~~~~~~~~~~~~~~ -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 -genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': -genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] - 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; - | ^ -genepi.cpp:614:17: note: 'cancor1_pos' was declared here - 614 | int cancor1_pos; - | ^~~~~~~~~~~ -In file included from genoerr.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 189 | for( int a = 0; a < posshap1.size(); a++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for( int b = 0; b < posshap2.size(); b++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 225 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] - 610 | double pvalue = chiprobP(chisq,df); - | ~~~~~~~~^~~~~~~~~~ -glm.cpp:556:15: note: 'df' was declared here - 556 | int df; - | ^~ -genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 315 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 347 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 358 | for (int z2=0; z2::__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; + | ^~~~~~~~~ +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 whap.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp +genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': +genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] + 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; + | ^ +genepi.cpp:614:17: note: 'cancor1_pos' was declared here + 614 | int cancor1_pos; + | ^~~~~~~~~~~ +In file included from 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 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 nonfounderphasing.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 105 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -impute.cpp: In member function 'void HaploPhase::mainImputation()': -impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 313 | for (int s=0; s < g.size(); s++) - | ~~^~~~~~~~~~ -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; - | ^~~~ -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 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 em.cpp:27: +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] - 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] 166 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3051,7 +3082,47 @@ clumpld.cpp:204:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 whap.cpp +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] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 189 | for( int a = 0; a < posshap1.size(); a++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 190 | for( int b = 0; b < posshap2.size(); b++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 225 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 315 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~ +genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 328 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 347 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 358 | for (int z2=0; z2&)': +nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] + 715 | double posterior = ip->second; + | ^~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) @@ -3065,55 +3136,90 @@ clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~ 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 simul.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 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 profile.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from impute.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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; + | ^~ +In file included from impute.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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++) | ~~^~~~~~~~~~~~~~~~~~ -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 +impute.cpp: In constructor 'probabilisticGenotype::probabilisticGenotype()': +impute.cpp:40:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 40 | phased = genotype = false; + | ~~~~~~~~~^~~~~~~ +impute.cpp: In member function 'void HaploPhase::updateForImputation()': +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; zgetStatistic() : 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() ) + | ~~~~~^~~~~~~~~~~~~~~~ +impute.cpp:144:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp: In member function 'void HaploPhase::mainImputation()': +impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 313 | for (int s=0; s < g.size(); s++) + | ~~^~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp 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] @@ -3123,36 +3229,48 @@ 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&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': +profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] + 480 | bool a1 = i2->second; + | ^~ +profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] + 525 | bool sawNamedAllele = false; + | ^~~~~~~~~~~~~~ +profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': +profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from profile.cpp:23: +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 helper.h:24, + from nlist.h:21, + from nlist.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ -merge.cpp:943:8: note: 'write' was declared here - 943 | bool write; - | ^~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 ) | ~~^~~~~~~~~~~~~~~ -profile.cpp: In member function 'void Plink::scoreIndividuals()': -profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] - 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] - 304 | bool OLD_clist = par::clist; - | ^~~~~~~~~ -profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] - 350 | double statistic = valid ? model->getStatistic() : 0; - | ^~~~~~~~~ -profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] - 351 | double pvalue = pval[ pval.size()-1 ]; - | ^~~~~~ -profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] - 352 | double beta = b[ b.size()-1 ]; - | ^~~~ -profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 390 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 402 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 421 | if ( qcnt == qlabel.size() ) - | ~~~~~^~~~~~~~~~~~~~~~ -profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': -profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] - 480 | bool a1 = i2->second; - | ^~ -profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] - 525 | bool sawNamedAllele = false; - | ^~~~~~~~~~~~~~ -profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': -profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 whap.cpp:20: + 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++) | ~~^~~~~~~~~~~~~~~~~~ +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] @@ -3245,7 +3360,6 @@ whap.cpp:334:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -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 whap.cpp:393:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 393 | for (int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~ +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] + 679 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ +simul.cpp: In member function 'void Plink::simulateSNPs_QT()': +simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 962 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1048 | for ( int i = 0 ; i < tok.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 idhelp.cpp whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1118 | if ( mapping.size() != H->ns + H->nh ) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ @@ -3313,7 +3443,6 @@ whap.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1290 | for (int g=0; g< model.group.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~ -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 whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1326 | for (int c=0; c < P->conditioner.size(); c++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3331,6 +3460,21 @@ 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() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +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; + | ^~~~ +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: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; @@ -3344,7 +3488,25 @@ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ -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 +greport.cpp: In member function 'void Plink::displayGeneReport()': +greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 147 | if ( tokens.size() <= chr_column || + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 148 | tokens.size() <= bp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 156 | if ( tokens.size() <= pval_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 169 | if ( tokens.size() <= snp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 240 | for (int l=0; l< ari->second.size(); l+=2) + | ~^~~~~~~~~~~~~~~~~~~~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ @@ -3360,6 +3522,9 @@ cnv.cpp:922:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 922 | isection.clear(); | ^~~~~~~~ +greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] + 125 | int cnt = 0; + | ^~~ cnv.cpp:1031:32: warning: variable 'i2' set but not used [-Wunused-but-set-variable] 1031 | set::iterator i2 = isection.begin(); | ^~ @@ -3372,6 +3537,7 @@ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] 412 | int nseg=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 tag.cpp cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; @@ -3396,140 +3562,31 @@ 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 || - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 148 | tokens.size() <= bp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 156 | if ( tokens.size() <= pval_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 169 | if ( tokens.size() <= snp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 240 | for (int l=0; l< ari->second.size(); l+=2) - | ~^~~~~~~~~~~~~~~~~~~~ -greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] - 125 | int cnt = 0; - | ^~~ -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 /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:1307:21, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: -/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bmerge.cpp: In member function 'void Plink::mergeBinaryData()': -bmerge.cpp:682:16: note: 'indn' was declared here - 682 | int indn; - | ^~~~ In file included from helper.h:24, - from simul.cpp:16: + 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 idhelp.cpp -In file included from helper.h:24, - from gvar.cpp:15: +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 tag.cpp In file included from helper.h:24, - from cnvqt.cpp:22: + 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++) | ~~^~~~~~~~~~~~~~~~~~ -simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': -simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] - 172 | double gh_11_12 = h11*h12; - | ^~~~~~~~ -simul.cpp: In member function 'void Plink::simulateSNPs()': -simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 679 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1211 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, - from flip.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++) @@ -3554,6 +3611,10 @@ 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 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 In file included from idhelp.cpp:18: @@ -3561,8 +3622,8 @@ 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++) @@ -3572,24 +3633,19 @@ 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 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++) - | ~~^~~~~~~~~~~~~~~~~~ -qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': -qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] - 122 | long int nfound = 0; - | ^~~~~~ -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 blox.cpp +setscreen.cpp: In member function 'void Plink::setAssocSummary()': +setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 80 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 110 | if ( tokens.size() != cols ) + | ~~~~~~~~~~~~~~^~~~~~~ +setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) + | ~~^~~~~~~~~~~~~~~~~~~ +setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int i=0; i < snpset[j].size(); i++) + | ~~^~~~~~~~~~~~~~~~~~ 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++) @@ -3614,10 +3670,6 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'bool RCount::addSNP(int)': -elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] - 374 | double wt; - | ^~ 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++) | ~~^~~~~~~~~~~~~ @@ -3628,11 +3680,24 @@ idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ +elf.cpp: In member function 'void Plink::elfBaseline()': +elf.cpp:1159:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] + 1159 | ++(*p_cnt); + | ~^~~~~~~ +elf.cpp:1111:13: note: 'p_cnt' was declared here + 1111 | int * p_cnt; + | ^~~~~ +elf.cpp:1153:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] + 1153 | ++(*p_gcnt); + | ~^~~~~~~~ +elf.cpp:1112:13: note: 'p_gcnt' was declared here + 1112 | int * p_gcnt; + | ^~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 502 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ -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 idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 510 | if ( p < tokens.size() ) | ~~^~~~~~~~~~~~~~~ @@ -3645,11 +3710,9 @@ idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.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 idhelp.cpp:529:24: warning: unused variable 'seenJoint' [-Wunused-variable] 529 | bool seenJoint = true; | ^~~~~~~~~ -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 idhelp.cpp:584:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 584 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ @@ -3689,11 +3752,9 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -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: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++) | ~~^~~~~~~~~~~~~~~~~~ -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:888:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3739,17 +3800,6 @@ idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from lookup2.cpp:18: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from setscreen.cpp:21: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -3780,23 +3830,10 @@ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1440 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1551 | for ( int i=0; i >::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:1631:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ -setscreen.cpp: In member function 'void Plink::setAssocSummary()': -setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 80 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 110 | if ( tokens.size() != cols ) - | ~~~~~~~~~~~~~~^~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) - | ~~^~~~~~~~~~~~~~~~~~~ -setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int i=0; i < snpset[j].size(); i++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1903 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2201 | for (int k = 0 ; k < thisLine.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 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++ ) @@ -3902,77 +3925,64 @@ 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 zfstream.cpp -proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] - 422 | int ref; - | ^~~ +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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp In file included from helper.h:24, - from zed.cpp:19: + from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~ In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from Rconnection.cpp:30: -Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': -Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 203 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -Rconnection.cpp: At global scope: -Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ - | ^~~~~~~~~~~~~~ -In file included from annot.cpp:20: +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++) | ~~^~~~~~~~~~~~~~~~~~ -Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': -Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 567 | if (host) free(host); host=0; - | ^~ -Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 567 | if (host) free(host); host=0; - | ^~~~ -In file included from hapglm.cpp:25: +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp +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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 blox.cpp: In member function 'std::map > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; @@ -3995,38 +4005,22 @@ blox.cpp:427:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 427 | for (int k=0; k >::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 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ blox.cpp: In member function 'void PairwiseLinkage::calculateCI()': blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ -annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] - 300 | bool include = false; - | ^~~~~~~ -In file included from r.cpp:29: +proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] + 422 | int ref; + | ^~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from Rconnection.cpp:30: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 203 | { name=""; fix_content(); } @@ -4046,29 +4040,49 @@ Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ -r.cpp: In member function 'void Plink::Rfunc()': -r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] - 330 | int ct = data->length(); - | ^~ -In file included from dosage.cpp:20: +Rconnection.cpp: At global scope: +Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ + | ^~~~~~~~~~~~~~ +Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': +Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 567 | if (host) free(host); host=0; + | ^~ +Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 567 | if (host) free(host); host=0; + | ^~~~ +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 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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from dosage.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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -dosage.cpp: In member function 'void Plink::processDosageFile()': -dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 110 | for ( int q = 0 ; q < qthresh.size() ; q++) - | ~~^~~~~~~~~~~~~~~~ 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; @@ -4079,9 +4093,6 @@ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] 61 | Alleles(string name, int chr, int bp, string a1, string a2) | ^~~~~~~ -dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 513 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 159 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 213 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 548 | for (int f = 0 ; f < vzin.size() ; f++ ) - | ~~^~~~~~~~~~~~~ metaanal.cpp:235:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 581 | if ( tok.size() < firstCol ) - | ~~~~~~~~~~~^~~~~~~~~~ -dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 601 | for (int i=firstCol; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ -dosage.cpp:695:29: 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 < personMap[f].size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~~~ -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 dosage.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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 482 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 680 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +dosage.cpp: 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++) + | ~~^~~~~~~~~~~~~~~~ +dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 513 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 548 | for (int f = 0 ; f < vzin.size() ; f++ ) + | ~~^~~~~~~~~~~~~ +dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 581 | if ( tok.size() < firstCol ) + | ~~~~~~~~~~~^~~~~~~~~~ +dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 601 | for (int i=firstCol; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 695 | for (int i = 0; i < personMap[f].size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~~~ +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 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) { + | ~~^~~~~ +dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 989 | for (int q=0; qgetStatistic() : 0; | ^~~~~~~~~ dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1252 | if ( o->second != dosageFilename_all.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +r.cpp: In member function 'void Plink::Rfunc()': +r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] + 330 | int ct = data->length(); + | ^~ dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1310 | if ( ++qq == qthresh.size() ) | ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] 190 | int geno_field = a2_field + skip2 + 1; | ^~~~~~~~~~ -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; - | ^~~~ +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; + | ^~~ r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -4179,49 +4252,6 @@ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ -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; - | ^~~~~~ -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; - | ^~~ -dosage.cpp:915:35: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] - 915 | SNP[snp_code]->one[personPosition[f][i]] = s1; - | ^ -dosage.cpp:725:15: note: 'snp_code' was declared here - 725 | int snp_code; - | ^~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) @@ -4229,6 +4259,12 @@ 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; + | ^ +dosage.cpp:725:15: note: 'snp_code' was declared here + 725 | int snp_code; + | ^~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with '-fvar-tracking-assignments', retrying without 80 | void setOptions(CArgs & a) @@ -4276,12 +4312,14 @@ 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/1353141/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1353141/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/1451901 and its subdirectories -I: Current time: Tue Sep 29 05:39:17 -12 2026 -I: pbuilder-time-stamp: 1790703557 +I: removing directory /srv/workspace/pbuilder/1353141 and its subdirectories +I: Current time: Thu Aug 28 01:18:26 +14 2025 +I: pbuilder-time-stamp: 1756293506