Diff of the two buildlogs: -- --- b1/build.log 2025-03-04 12:19:52.363057013 +0000 +++ b2/build.log 2025-03-04 12:22:45.671240775 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 6 06:41:18 -12 2026 -I: pbuilder-time-stamp: 1775500878 +I: Current time: Wed Mar 5 02:19:55 +14 2025 +I: pbuilder-time-stamp: 1741090795 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,51 +27,83 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3718522/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3380717/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 4 12:20 /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/3380717/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3380717/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' + 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=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1c18ab4f0a864e88bc0f03e5319cdaf8' - 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='3718522' - PS1='# ' - PS2='> ' + INVOCATION_ID=4be94cd529df4eef91aee7d3efa435a0 + 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=3380717 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.uRXHfaZC/pbuilderrc_Fze2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uRXHfaZC/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.uRXHfaZC/pbuilderrc_Djt1 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uRXHfaZC/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3718522/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3380717/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 21.5 MB in 1s (16.1 MB/s) +Fetched 21.5 MB in 5s (4734 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 ... 19802 files and directories currently installed.) @@ -279,7 +311,11 @@ 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/3380717/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3380717/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 @@ -320,23 +356,51 @@ 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 locus.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 multi.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 cluster.cpp -In file included from locus.cpp:16: +In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from input.cpp:24: +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp +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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from options.cpp:16: +In file included from locus.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from multi.cpp:16: +tinput.cpp: In member function 'void Plink::readTransposedData()': +tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 309 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | if ( c > sample.size()) + | ~~^~~~~~~~~~~~~~~ +tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ +In file included from input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -367,30 +431,6 @@ input.cpp:695:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 695 | for (int i=0; i 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; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 787 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from filters.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ input.cpp:1374:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ @@ -473,82 +503,13 @@ 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] - 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] 1764 | for (int c=0; c::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] 1792 | 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -binput.cpp:339:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -binput.cpp:398:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -filters.cpp:273:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] - 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2225 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ -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] 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2471 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 739 | for ( int l = 0 ; l < locus.size() ; l++ ) - | ~~^~~~~~~~~~~~~~ -filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 762 | for ( int i = 0 ; i < sample.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::updateAlleles()': +input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] + 2732 | bool success = 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 mds.cpp +In file included from genome.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from 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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from filters.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:15: warning: unused variable 'geno_nm' [-Wunused-variable] 99 | int geno_nm = 0; @@ -604,49 +574,10 @@ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] 81 | double tothet = 0; | ^~~~~~ -input.cpp: In member function 'void Plink::updateAlleles()': -input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] - 2732 | bool success = false; - | ^~~~~~~ -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] - 1078 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1091 | for (int l=0; lfreq * ( 1 - locus[l]->freq ); | ^~ -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&, std::vector&, std::vector >&)': -stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] - 458 | int m,l,iter,i,k; - | ^ -filters.cpp:1165:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1165 | for ( int i=0; i > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ 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; @@ -661,23 +592,102 @@ genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 1067 | if ( (!par::silent ) && c==c2 || c==np) | ~~~~~~~~~~~~~~~~^~~~~~~~ -filters.cpp: In member function 'void Plink::thinSNPs()': -filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] - 1277 | int x = 0; +genome.cpp: In member function 'void Plink::pruneLD()': +genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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] + 273 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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++ ) + | ~~^~~~~~~~~~~~~~~ +In file included from binput.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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; + | ^ +stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': +stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] + 813 | const double eps = 1e-12; + | ^~~ +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 > msqrt(std::vector >&)': +stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] + 906 | const double eps = 1e-12; + | ^~~ +In file included from plink.cpp:28: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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] 1477 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::pruneLD()': -genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1483 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ @@ -691,52 +701,60 @@ 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++) | ~~^~~~~~~~~~ -genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] - 1189 | int win_end = win_start + par::prune_ld_win; - | ^~~~~~~ +filters.cpp: In member function 'void Plink::thinSNPs()': +filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] + 1277 | int x = 0; + | ^ +binput.cpp: In member function 'void Plink::readBinData()': +binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i 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] + 157 | 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] + 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 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++) | ~~^~~~~~~~~~~~~~~~~~ -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) - | ~~~~~~~~~~~~~~~~~~~~ -tinput.cpp: In member function 'void Plink::readTransposedData()': -tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 271 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 309 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 591 | if ( c > sample.size()) - | ~~^~~~~~~~~~~~~~~ -tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ -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 >&)': 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] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ -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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 323 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 461 | for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 659 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ +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] 959 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::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'} and 'int' [-Wsign-compare] 1264 | if (sample[i]->fid.length() > par::pp_maxfid) @@ -911,7 +949,6 @@ helper.cpp:2606:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2606 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i * s; | ^ +In file included from helper.h:24, + from cluster.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] 3324 | int last = -1; @@ -948,12 +991,6 @@ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] 3329 | int nextChromosome; | ^~~~~~~~~~~~~~ -In file included from helper.h:24, - from cluster.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) @@ -1078,7 +1115,29 @@ 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +mds.cpp: In member function 'void Plink::generateMDS()': +mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ +In file included from output.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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); @@ -1107,30 +1166,6 @@ helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 informative.cpp -In file included from mds.cpp:21: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -mds.cpp: In member function 'void Plink::generateMDS()': -mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] - 242 | bool flag = svd(D,eigenvalue,eigenvector); - | ^~~~ -In file included from output.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1200,7 +1236,6 @@ | ~^~~~~~~~~~~~~~ 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 assoc.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -1240,41 +1275,18 @@ /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_pairList()': -output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] - 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:11: note: 'i2' was declared here - 116 | int i1, i2; - | ^~ -output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:7: note: 'i1' was declared here - 116 | int i1, i2; - | ^~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp 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 prephap.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int i=0; iprofileSNPs.size(); i++) @@ -1291,36 +1303,24 @@ 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++) | ~^~~~~~~~~~~~~~~~~~~~~ -prephap.cpp: In member function 'void HaploPhase::readTagFile()': -prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 226 | if (len != tokens.size() - offset ) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | for ( int i = allele ; i < tokens.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 412 | while ( index < tokens.size() ) - | ~~~~~~^~~~~~~~~~~~~~~ -prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 416 | if ( tokens[index].size() != len ) - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ -prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 420 | if ( index == tokens.size() - 1 ) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ +output.cpp: In member function 'void Plink::display_pairList()': +output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] + 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:11: note: 'i2' was declared here + 116 | int i1, i2; + | ^~ +output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] + 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:7: note: 'i1' was declared here + 116 | int i1, i2; + | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1344,27 +1344,56 @@ | ^ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp +In file included from prephap.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_indivReport()': -output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 69 | << setw(6) << genotype(*this,i1,l) << "\n"; - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:46:7: note: 'i1' was declared here - 46 | int i1; - | ^~ +In file included from prephap.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 226 | if (len != tokens.size() - offset ) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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] + 283 | for ( int i = allele ; i < tokens.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ genogroup.h: In member function 'bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const': genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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 ) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 470 | for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 533 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1446,6 +1475,13 @@ 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 871 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ trio.cpp:936:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 936 | for (int f=0;f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from tdt.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~ 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++) @@ -1535,8 +1567,26 @@ 776 | for (int f=0; f 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 perm.h:17, + from sharing.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': +sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int l=0; l 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 ) @@ -1544,19 +1594,51 @@ assoc.cpp:1019:14: note: 'pvalue' was declared here 1019 | double pvalue; | ^~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp +In file included from /usr/include/c++/14/iostream:41, + from assoc.cpp:14: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: +/usr/include/c++/14/ostream:232:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1385:22: note: 'mult_chisq' was declared here + 1385 | double mult_p, mult_chisq; + | ^~~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: +/usr/include/c++/14/ostream:232:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:14: note: 'dom_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: +/usr/include/c++/14/ostream:232:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:25: note: 'rec_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: +/usr/include/c++/14/ostream:232:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:36: note: 'gen_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ In file included from genepi.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from perm.h:17, - from sharing.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp 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 | } @@ -1582,10 +1664,6 @@ genepi.cpp:507:17: warning: unused variable 'ne' [-Wunused-variable] 507 | int ne = n1 < n2 ? n1 : n2; | ^~ -sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': -sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 102 | for (int l=0; l >&, 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::__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 perm.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp 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] @@ -1760,19 +1796,37 @@ sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': +mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': +mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1249 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readData()': +input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] + 91 | if ( feof(PED) ) + | ~~~~^~~~~ +input.cpp:60:10: note: 'PED' was declared here + 60 | FILE * PED; + | ^~~ 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] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ -mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': -mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': -mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1249 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] - 91 | if ( feof(PED) ) - | ~~~~^~~~~ -input.cpp:60:10: note: 'PED' was declared here - 60 | FILE * PED; - | ^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 merge.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp -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; - | ^~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp 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] @@ -1877,6 +1904,28 @@ 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 >&, Set&, Plink&)': +genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] + 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; + | ^ +genepi.cpp:614:17: note: 'cancor1_pos' was declared here + 614 | int cancor1_pos; + | ^~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp +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++) + | ~~^~~~~~~~~~~~~~~~~~ +hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': +hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 77 | if (!sample[i]->missing) + | ^ +hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 173 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': -hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 77 | if (!sample[i]->missing) - | ^ -hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 173 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp 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] @@ -1944,6 +1980,7 @@ 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp 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] @@ -1954,36 +1991,7 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp -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] - 195 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 198 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ -poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': -poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 293 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -linear.cpp: In member function 'virtual void LinearModel::pruneY()': -linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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; - | ^~~~~ 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++) @@ -2062,63 +2047,64 @@ qfam.cpp:657:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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++) - | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] 639 | int tc = 0; | ^~ -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] - 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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from mishap.cpp:17: +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 +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] + 195 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 198 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ +poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': +poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 293 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 328 | for (int c=0; c, int>&)': +merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] + 1103 | if (write) + | ^~ +merge.cpp:943:8: note: 'write' was declared here + 943 | bool write; + | ^~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp +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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from homozyg.cpp:23: +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] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -2141,6 +2127,17 @@ 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 parse.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from homozyg.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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++) @@ -2157,6 +2154,11 @@ 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++) | ~~^~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~ @@ -2179,15 +2181,16 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~ +homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': +homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] + 2155 | homozygWindows[l] == 0; +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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; 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] 480 | 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] + 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] + 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from model.cpp:17: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i&)': -model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 132 | if ( include.size() != P->n ) - | ~~~~~~~~~~~~~~~^~~~~~~ -model.cpp: In member function 'void Model::buildDesignMatrix()': -model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 354 | for (int i=0; i< par::parameter_list.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 367 | for ( int i = 0 ; i < X.size() ; i++) - | ~~^~~~~~~~~~ -model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'bool Model::checkVIF()': -model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] - 613 | double maxVIF = 0; - | ^~~~~~ In file included from helper.h:24, from 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 helper.h:24, - from logistic.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from 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&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2319,20 +2332,24 @@ segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void Model::setMissing(std::vector&)': +model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 132 | if ( include.size() != P->n ) + | ~~~~~~~~~~~~~~~^~~~~~~ +model.cpp: In member function 'void Model::buildDesignMatrix()': +model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 354 | for (int i=0; i< par::parameter_list.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 367 | for ( int i = 0 ; i < X.size() ; i++) + | ~~^~~~~~~~~~ +model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'bool Model::checkVIF()': +model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] + 613 | double maxVIF = 0; + | ^~~~~~ segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] 1855 | indivPair p = ic->first; @@ -2378,6 +2395,30 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ +linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': +linear.cpp:96:5: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] + 96 | if (irow != icol) { + | ^~ +linear.cpp:75:9: note: 'icol' was declared here + 75 | int i,icol,irow,j,k,l,ll; + | ^~~~ +linear.cpp:96:5: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] + 96 | if (irow != icol) { + | ^~ +linear.cpp:75:14: note: 'irow' was declared here + 75 | int i,icol,irow,j,k,l,ll; + | ^~~~ +In file included from helper.h:24, + from glm.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp +model.cpp: In member function 'double Model::buildQFAM(Individual*)': +model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] + 849 | error("Internal problem with QFAM model specification"); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] @@ -2396,12 +2437,6 @@ glm.cpp:423:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 423 | for (int c=0; c *xn)) goto S160; @@ -2438,21 +2473,61 @@ dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp -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 dfam.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 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++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from fisher.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 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++) @@ -2481,44 +2556,6 @@ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ -In file included from helper.h:24, - from fisher.cpp:17: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from linput.cpp:25: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from dfam.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 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 /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from bmerge.cpp:14: -In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, - inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: -/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bmerge.cpp: In member function 'void Plink::mergeBinaryData()': -bmerge.cpp:682:16: note: 'indn' was declared here - 682 | int indn; - | ^~~~ +glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] + 610 | double pvalue = chiprobP(chisq,df); + | ~~~~~~~~^~~~~~~~~~ +glm.cpp:556:15: note: 'df' was declared here + 556 | int df; + | ^~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp In file included from helper.h:24, from 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 lookup.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 @@ -2670,6 +2656,37 @@ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] 119 | int echoStringLen = 100; | ^~~~~~~~~~~~~ +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] + 209 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 289 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ -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 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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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] 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 haploQTL.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, int, bool)': +haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 83 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ proxy.cpp: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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2729,60 +2772,102 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp -In file included from pdriver.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:575:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, + inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: +/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bmerge.cpp: In member function 'void Plink::mergeBinaryData()': +bmerge.cpp:682:16: note: 'indn' was declared here + 682 | int indn; + | ^~~~ +In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploQTL.cpp:25: +In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, 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 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 -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 haplowindow.cpp:28: +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] + 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': +haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 558 | for (int z=0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 574 | for (int z=0; z < new_pp.size(); z++) + | ~~^~~~~~~~~~~~~~~ +haplowindow.cpp: In member function 'void HaploWindow::performEM()': +haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 683 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 691 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 751 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 791 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 798 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 868 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 872 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 949 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 966 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 -elf.cpp: In member function 'void Plink::elfBaseline()': -elf.cpp:1159:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] - 1159 | ++(*p_cnt); - | ~^~~~~~~ -elf.cpp:1111:13: note: 'p_cnt' was declared here - 1111 | int * p_cnt; - | ^~~~~ -elf.cpp:1153:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] - 1153 | ++(*p_gcnt); - | ~^~~~~~~~ -elf.cpp:1112:13: note: 'p_gcnt' was declared here - 1112 | int * p_gcnt; - | ^~~~~~ In file included from 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] @@ -2797,7 +2882,6 @@ 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from haplowindow.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 haplowindow.cpp:27: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': -haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 558 | for (int z=0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 574 | for (int z=0; z < new_pp.size(); z++) - | ~~^~~~~~~~~~~~~~~ -haplowindow.cpp: In member function 'void HaploWindow::performEM()': -haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 683 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 691 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 751 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 791 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 798 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 868 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 872 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 949 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 966 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2962,8 +2982,6 @@ 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2978,25 +2996,12 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ 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] 668 | for (int z=0; z < pp[i].size(); z++) @@ -3008,36 +3013,22 @@ nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ -In file included from genoerr.cpp:28: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 189 | for( int a = 0; a < posshap1.size(); a++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for( int b = 0; b < posshap2.size(); b++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 225 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 315 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 347 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 358 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 92 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 189 | for( int a = 0; a < posshap1.size(); a++ ) + | ~~^~~~~~~~~~~~~~~~~ clumpld.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] + 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++) + | ~~^~~~~~~~~~~~~~~~~ clumpld.cpp:137:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 137 | for ( int f=0; f >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +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] 201 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 347 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 358 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~ -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] 480 | if( l1 < P->locus.size()-1 ) | ~~~^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ -In file included from em.cpp:28: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ -em.cpp: In member function 'void HaploPhase::performEM_original()': -em.cpp:89:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 97 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 106 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 128 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 132 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 162 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 166 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from metaem.cpp:24: +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 metaem.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp +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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from metaem.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp -metaem.cpp: In member function 'void HaploPhase::enumeratePhasedWindows(int)': -metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 239 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3194,6 +3174,43 @@ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ +In file included from 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] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 97 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 106 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 128 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 132 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 162 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 166 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3224,6 +3241,13 @@ profile.cpp:421:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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; @@ -3234,25 +3258,14 @@ 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++) - | ~~^~~~~~~~~~~~~~~~~~ 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&, std::map >&, std::map&, std::ofstream&)': +profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 667 | for (int l=0; l NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -In file included from helper.h:24, - from whap.cpp:20: +In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from metaem.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3361,6 +3398,12 @@ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from simul.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1334 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ whap.cpp: In function 'void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)': whap.cpp:1425:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1425 | for (int h=0; h < m.group.size(); h++) @@ -3375,13 +3424,28 @@ 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() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ -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 helper.h:24, - from gvar.cpp:15: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp +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] 556 | 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 step.cpp -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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; @@ -3469,12 +3510,6 @@ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ -In file included from helper.h:24, - from step.cpp:18: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ @@ -3496,11 +3531,6 @@ cnv.cpp:1103:43: warning: variable 'il' set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ -In file included from greport.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ @@ -3511,22 +3541,6 @@ cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; | ^~~ -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 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2013 | for (int c = 0 ; c < scaffold.size(); c++) @@ -3538,9 +3552,6 @@ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] 2202 | indivPair p = ic->first; | ^ -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:2288:10: warning: unused variable 'statistic' [-Wunused-variable] 2288 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ @@ -3550,16 +3561,50 @@ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.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 cnvqt.cpp +In file included from helper.h:24, + from flip.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 cnvqt.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp +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 qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3570,26 +3615,29 @@ qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ -In file included from helper.h:24, - from cnvqt.cpp:22: +In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp +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++) + | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from idhelp.cpp:18: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) @@ -3610,6 +3658,13 @@ 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++) | ~~^~~~~~~~~~~~~ +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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp +In file included from idhelp.cpp:18: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3622,13 +3677,6 @@ idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 63 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp idhelp.cpp: In member function 'bool IDHelper::matchIndividual(IDGroup*, std::map >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) @@ -3652,23 +3700,10 @@ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] 214 | vector & jo = jointOrder[j]; | ^~ -setscreen.cpp: In member function 'void Plink::setAssocSummary()': -setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 80 | for (int i=0; i IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ -setscreen.cpp:110:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 110 | if ( tokens.size() != cols ) - | ~~~~~~~~~~~~~~^~~~~~~ -setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) - | ~~^~~~~~~~~~~~~~~~~~~ -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 '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() ) @@ -3848,6 +3883,7 @@ idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 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) @@ -3882,6 +3918,7 @@ 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -3894,6 +3931,12 @@ idhelp.cpp:2201:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2201 | for (int k = 0 ; k < thisLine.size() ; k++ ) | ~~^~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from tag.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: 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++ ) @@ -3901,31 +3944,32 @@ 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 zed.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp In file included from helper.h:24, - from tag.cpp:24: + from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from hapglm.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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 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 hapglm.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) @@ -3939,70 +3983,18 @@ 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 dosage.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from zed.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp -In file included from 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] - 110 | for ( int q = 0 ; q < qthresh.size() ; q++) - | ~~^~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ -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] ) -dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 989 | for (int q=0; qgetStatistic() : 0; - | ^~~~~~~~~ -dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1252 | if ( o->second != dosageFilename_all.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1310 | if ( ++qq == qthresh.size() ) - | ~~~~~^~~~~~~~~~~~~~~~~ -dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] - 190 | int geno_field = a2_field + skip2 + 1; - | ^~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; @@ -4032,36 +4024,6 @@ blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp -In file included from annot.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp -annot.cpp: In member function 'void Plink::annotateFile()': -annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 250 | if ( tokens.size() <= chr_column || - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 251 | tokens.size() <= bp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 260 | if ( tokens.size() <= pval_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 275 | if ( tokens.size() <= snp_column ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] - 300 | bool include = false; - | ^~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp In file included from 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] @@ -4090,6 +4052,28 @@ metaanal.cpp:213:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 213 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 300 | if ( tokens.size() != fsize ) + | ~~~~~~~~~~~~~~^~~~~~~~ +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 +metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] + 253 | int pval_column = -1; + | ^~~~~~~~~~~ +metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 680 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 300 | if ( tokens.size() != fsize ) - | ~~~~~~~~~~~~~~^~~~~~~~ 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 */ @@ -4130,42 +4105,16 @@ 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; | ^~~~ -metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] - 253 | int pval_column = -1; - | ^~~~~~~~~~~ -metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 680 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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; ilength(); | ^~ +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] ) +dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +dosage.cpp:1170:18: warning: unused variable 'statistic' [-Wunused-variable] + 1170 | double statistic = valid ? model->getStatistic() : 0; + | ^~~~~~~~~ +dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1252 | if ( o->second != dosageFilename_all.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1310 | if ( ++qq == qthresh.size() ) + | ~~~~~^~~~~~~~~~~~~~~~~ +dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] + 190 | int geno_field = a2_field + skip2 + 1; + | ^~~~~~~~~~ +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; jassign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -4226,6 +4220,48 @@ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ +annot.cpp:149:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} 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; + | ^~~~~~~ +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; | ^ @@ -4279,12 +4315,14 @@ 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/3380717/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3380717/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/3718522 and its subdirectories -I: Current time: Mon Apr 6 06:42:51 -12 2026 -I: pbuilder-time-stamp: 1775500971 +I: removing directory /srv/workspace/pbuilder/3380717 and its subdirectories +I: Current time: Wed Mar 5 02:22:44 +14 2025 +I: pbuilder-time-stamp: 1741090964