Diff of the two buildlogs: -- --- b1/build.log 2023-05-06 02:47:52.633341782 +0000 +++ b2/build.log 2023-05-06 03:30:31.797171396 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 5 14:34:49 -12 2023 -I: pbuilder-time-stamp: 1683340489 +I: Current time: Fri Jun 7 23:11:06 +14 2024 +I: pbuilder-time-stamp: 1717751466 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Oct 31 03:36:45 2021 -12 +gpgv: Signature made Mon Nov 1 05:36:45 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -31,52 +31,84 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29555/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/31576/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-arm64. +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 Jun 7 23:11 /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/31576/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/31576/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='29555' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=31576 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.VTBpSLxw/pbuilderrc_7zMn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/pbuilderrc_sW1Z --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/b2 --logfile b2/build.log --extrapackages usrmerge plink_1.07+dfsg-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink10-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 4 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/29555/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 6 06:49 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/31576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -145,7 +177,7 @@ Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 19.3 MB in 0s (47.4 MB/s) +Fetched 19.3 MB in 1s (22.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19616 files and directories currently installed.) @@ -283,8 +315,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/31576/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/31576/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -321,11 +362,62 @@ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp +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 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 input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from 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++) + | ~~^~~~~~~~~~~~~~~~~~ +binput.cpp: In member function 'void Plink::readBinData()': +binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +In file included from helper.h:24, + from 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 516 | if ( i == include.size() ) @@ -348,30 +440,76 @@ input.cpp:631:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from helper.cpp:24: +tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 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] + 695 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 591 | if ( c > sample.size()) + | ~~^~~~~~~~~~~~~~~ +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() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::string display(std::vector >&)': +helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 58 | for (int i=0; i >&)': +helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 76 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 79 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 90 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ +helper.cpp: In function 'void display(std::vector&)': +helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 100 | for (int i=0; i< m.size(); i++) + | ~^~~~~~~~~~ input.cpp:817:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ @@ -382,6 +520,13 @@ input.cpp:897:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 897 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 927 | for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1261 | for (int i0=0; i0freq * ( 1 - locus[l]->freq ); + | ^~ +stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': +stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] + 458 | int m,l,iter,i,k; + | ^ input.cpp: In member function 'bool Plink::readCovListFile()': input.cpp:1335:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'std::string display(std::vector >&)': -helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 58 | for (int i=0; i >&)': -helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 76 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 79 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 90 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -helper.cpp: In function 'void display(std::vector&)': -helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 100 | for (int i=0; i< m.size(); i++) - | ~^~~~~~~~~~ -input.cpp:1519:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1599 | else if (tokens.size() != par::plist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] - 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1792 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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++) - | ~~^~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2225 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readFamFile(std::string)': -input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': +stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] + 813 | const double eps = 1e-12; + | ^~~ +stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] + 818 | int r = u.size(); + | ^ +stats.cpp: In function 'std::vector > msqrt(std::vector >&)': +stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] + 906 | const double eps = 1e-12; + | ^~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i > CArgs::value(std::string, int)': helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) @@ -556,6 +593,16 @@ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); | ~~~~~~~~~^~~~ +genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': +genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] + 843 | double e10 = E10*S; + | ^~~ +genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] + 844 | double e20 = E20*S; + | ^~~ +genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] + 848 | double e21 = E21*S; + | ^~~ helper.cpp: In function 'std::vector > parse2str(std::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 306 | for (int i=0 ; i < s.length() ; i++) @@ -570,20 +617,41 @@ helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 323 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': +genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 1067 | if ( (!par::silent ) && c==c2 || c==np) + | ~~~~~~~~~~~~~~~~^~~~~~~~ +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 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': +stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1477 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1483 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1515 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1521 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp: In function 'matrix_t vec2diag(vector_t&)': +stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1531 | for (int i = 0; i < v.size(); i++) + | ~~^~~~~~~~~~ +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] 461 | for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 664 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1572 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1599 | else if (tokens.size() != par::plist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1602 | for (int i=0;i > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 709 | while(h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ +input.cpp:1745:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1792 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) @@ -637,13 +731,6 @@ helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1040 | for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1273 | if (locus[l]->name.length() > par::pp_maxsnp) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -plink.cpp: In function 'int main(int, char**)': -plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 763 | par::make_founders && - | ~~~~~~~~~~~~~~~~~~~^~ - 764 | !par::built_families) - | ~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1391 | for (int j=0; jfreq * ( 1 - locus[l]->freq ); - | ^~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': -genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] - 843 | double e10 = E10*S; - | ^~~ -genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] - 844 | double e20 = E20*S; - | ^~~ -genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] - 848 | double e21 = E21*S; - | ^~~ -genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': -genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 1067 | if ( (!par::silent ) && c==c2 || c==np) - | ~~~~~~~~~~~~~~~~^~~~~~~~ +In file included from plink.cpp:35: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2225 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readFamFile(std::string)': +input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2471 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; @@ -724,9 +832,6 @@ helper.cpp:2568:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2568 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2587 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2606 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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: 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] 2671 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2722 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2756 | for (int j=1; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2935 | for (int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ -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; - | ^~~ -stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] - 818 | int r = u.size(); - | ^ -stats.cpp: In function 'std::vector > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ +plink.cpp: In member function 'void Plink::cleanUp()': +plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2366 | for (int l=0; l, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; | ^ -stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': -stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1477 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1483 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1515 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1521 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp: In function 'matrix_t vec2diag(vector_t&)': -stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1531 | for (int i = 0; i < v.size(); i++) - | ~~^~~~~~~~~~ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] 3324 | int last = -1; @@ -883,11 +924,6 @@ helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from filters.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from stats.h:19, from stats.cpp:24: @@ -900,6 +936,11 @@ stats.cpp:1035:22: note: 'nm' was declared here 1035 | int i,its,j,jj,k,l,nm; | ^~ +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++) + | ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 95 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp 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] @@ -991,39 +1031,17 @@ multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] 155 | bool is1zero = IBDg.z1 < EPS ? true : false; | ^~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp -In file included from mds.cpp:21: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ -mds.cpp: In member function 'void Plink::generateMDS()': -mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 191 | for (int i2=0; i2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -mds.cpp:279:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] - 242 | bool flag = svd(D,eigenvalue,eigenvector); - | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp 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++) @@ -1052,16 +1070,6 @@ cluster.cpp:786:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 86 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 89 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j::iterator loc1 = locus.begin()+m1; - | ^~~~ -output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] - 403 | vector::iterator loc2 = locus.begin()+m2; - | ^~~~ cluster.cpp: In member function 'void Plink::groupGenome()': cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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++) + | ~~^~~~~~~~~~~~~~~~~~ +output.cpp: In member function 'void Plink::displayGenomePV()': +output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 86 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 89 | for (int k=0; k::iterator loc1 = locus.begin()+m1; + | ^~~~ +output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] + 403 | vector::iterator loc2 = locus.begin()+m2; + | ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 520 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::outputSetFile()': output.cpp:2200:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2200 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp 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] @@ -1327,10 +1368,6 @@ output.cpp:46:7: note: 'i1' was declared here 46 | int i1; | ^~ -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1405:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] - 1405 | int maxI; - | ^~~~ In file included from 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] @@ -1388,6 +1425,11 @@ phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ +helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1405:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] + 1405 | int maxI; + | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1109:68: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] 1109 | pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); @@ -1395,7 +1437,6 @@ assoc.cpp:1019:14: note: 'pvalue' was declared here 1019 | double pvalue; | ^~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) @@ -1515,6 +1556,7 @@ 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp In file included from 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] @@ -1564,16 +1606,9 @@ tdt.cpp:776:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -perm.cpp: In member function 'void Perm::permuteInCluster()': -perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 199 | for(int i=0; i&, std::vector&)': -perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int j=0;j< P.pS->snpset[l].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:936:40: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] + 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tdt.cpp:460:10: note: 'zt' was declared here + 460 | double zt; + | ^~ In file included from sets.cpp: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] @@ -1635,6 +1652,11 @@ sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 99 | for(int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneMC(Plink&, bool, double)': sets.cpp:129:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 129 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 618 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 703 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:713:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 713 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 975 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 905 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 975 | for (int k=0; k >&, Set&, Plink&)': genepi.cpp:489:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 489 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 497 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': genepi.cpp:1025:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1025 | for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp +perm.cpp: In member function 'void Perm::permuteInCluster()': +perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 199 | for(int i=0; i&, std::vector&)': +perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 273 | for (int j=0;j< P.pS->snpset[l].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from perm.h:17, from genedrop.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from perm.h:17, + from mh.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 64 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ -In file included from perm.h:17, - from mh.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 333 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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; smissing) + | ^ +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++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp In file included from 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] @@ -1925,16 +1970,6 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ -merge.cpp:943:8: note: 'write' was declared here - 943 | bool write; - | ^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp 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] @@ -1945,9 +1980,39 @@ 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++) + | ~~^~~~~~~~~~~~~~~~~~ +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; + | ^~~~~ +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++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from qfam.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++) | ~~^~~~~~~~~~~~~~~~~~ -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] 82 | for (int k=0; k < (*f)->kid.size() ;k++) @@ -2046,6 +2085,8 @@ linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp 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] @@ -2088,35 +2129,12 @@ bmerge.cpp:883:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 883 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from mishap.cpp:20: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from /usr/include/c++/12/vector:64, from linear.h:17, from linear.cpp:18: @@ -2138,6 +2156,29 @@ linear.cpp:75:9: note: 'icol' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ +In file included from mishap.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from mishap.cpp:20: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp In file included from helper.h:24, from legacy.cpp:22: @@ -2203,7 +2244,6 @@ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 756 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ @@ -2235,7 +2275,6 @@ 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp In file included from model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2246,12 +2285,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from plink.h:21, from legacy.cpp:21: @@ -2264,6 +2297,12 @@ legacy.cpp:35:7: note: 'last' was declared here 35 | int last; | ^~~~ +In file included from helper.h:24, + from segment.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 ) @@ -2282,12 +2321,6 @@ model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ -In file included from helper.h:24, - from logistic.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2315,14 +2348,7 @@ segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; ifirst; @@ -2368,35 +2394,26 @@ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ 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] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 294 | for (int h=1; h < whap->current->group.size(); h++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 423 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': +logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i *xn)) goto S160; @@ -2433,22 +2450,46 @@ dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from helper.h:24, + from glm.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from glm.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 294 | for (int h=1; h < whap->current->group.size(); h++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 423 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp 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++) @@ -2457,6 +2498,11 @@ elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 609 | for (int l=0; l< original.size(); l++) | ~^~~~~~~~~~~~~~~~~ +In file included from 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++) + | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] 654 | const double pthresh = 0.01; @@ -2477,11 +2523,6 @@ 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 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from fisher.cpp:17: +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] + 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++) | ~~^~~~~~~~~~~~~~~~~~ +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] @@ -2689,12 +2743,14 @@ proxy.cpp:332:29: warning: comparison of integer expressions of different signedness: 'std::set::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1401 | for (int c1 = 0; c1 < collection.size() ; c1++ ) | ~~~^~~~~~~~~~~~~~~~~~~ @@ -2704,26 +2760,17 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ -In file included from pdriver.cpp:16: +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp +In file included from haploQTL.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from pdriver.cpp: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++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp 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] @@ -2736,27 +2783,6 @@ 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++) | ~~^~~~~~~~~~~~~~~~ -elf.cpp: In member function 'void Plink::elfBaseline()': -elf.cpp:1142:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] - 1142 | ++(*p_gcnt); - | ~^~~~~~~~ -elf.cpp:1112:13: note: 'p_gcnt' was declared here - 1112 | int * p_gcnt; - | ^~~~~~ -elf.cpp:1147:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] - 1147 | ++(*p_cnt); - | ~^~~~~~~ -elf.cpp:1111:13: note: 'p_cnt' was declared here - 1111 | int * p_cnt; - | ^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp -In file included from haplohelper.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ 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] @@ -2771,6 +2797,7 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1477 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'void Plink::elfBaseline()': +elf.cpp:1142:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] + 1142 | ++(*p_gcnt); + | ~^~~~~~~~ +elf.cpp:1112:13: note: 'p_gcnt' was declared here + 1112 | int * p_gcnt; + | ^~~~~~ +elf.cpp:1147:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] + 1147 | ++(*p_cnt); + | ~^~~~~~~ +elf.cpp:1111:13: note: 'p_cnt' was declared here + 1111 | int * p_cnt; + | ^~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp In file included from 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] @@ -2872,11 +2912,6 @@ 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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) @@ -2921,6 +2956,12 @@ 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2935,6 +2976,7 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2954,13 +2996,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) @@ -2972,6 +3007,14 @@ nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp +In file included from helper.h:24, + from clumpld.h:21, + from clumpld.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3015,13 +3058,50 @@ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from genoerr.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 189 | for( int a = 0; a < posshap1.size(); a++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 190 | for( int b = 0; b < posshap2.size(); b++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 225 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +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::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator]', @@ -3038,15 +3118,6 @@ options.h:73:35: warning: comparison of integer expressions of 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] @@ -3061,11 +3132,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 166 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 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] 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 impute.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3156,11 +3202,6 @@ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ -In file included from metaem.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3232,6 +3273,7 @@ options.h:73:35: warning: comparison of integer expressions of 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 38 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24, - from simul.cpp:16: + from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -simul.cpp: In member function 'void Plink::simulateSNPs_QT()': -simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3347,6 +3367,10 @@ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1048 | for ( int i = 0 ; i < tok.size() ; i++ ) | ~~^~~~~~~~~~~~ +simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': +simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] + 172 | double gh_11_12 = h11*h12; + | ^~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1118 | if ( mapping.size() != H->ns + H->nh ) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ @@ -3368,6 +3392,13 @@ whap.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1290 | for (int g=0; g< model.group.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~ +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] 1326 | for (int c=0; c < P->conditioner.size(); c++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3385,13 +3416,24 @@ 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp +simul.cpp: In member function 'void Plink::simulateSNPs_QT()': +simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 125 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 192 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 247 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 556 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from step.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; @@ -3501,12 +3547,8 @@ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from 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] @@ -3534,15 +3576,13 @@ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3553,22 +3593,21 @@ qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) @@ -3589,34 +3628,23 @@ 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from idhelp.cpp:19: +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp +In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ -setscreen.cpp: In member function 'void Plink::setAssocSummary()': -setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 80 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 110 | if ( tokens.size() != cols ) - | ~~~~~~~~~~~~~~^~~~~~~ -setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) - | ~~^~~~~~~~~~~~~~~~~~~ -setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int i=0; i < snpset[j].size(); i++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) @@ -3624,6 +3652,13 @@ 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] + 80 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 110 | if ( tokens.size() != cols ) + | ~~~~~~~~~~~~~~^~~~~~~ idhelp.cpp: In member function '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++) @@ -3631,6 +3666,9 @@ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::map >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 169 | if ( found != matchTemplate.size() ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) + | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] 128 | bool match = true; | ^~~~~ @@ -3638,12 +3676,9 @@ idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ -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++) - | ~~^~~~~~~~~~~~~~~~~~ +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:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -3670,6 +3705,7 @@ idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 547 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ @@ -3682,12 +3718,6 @@ idhelp.cpp:594:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 594 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ -In file included from helper.h:24, - from hapglm.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 678 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ @@ -3724,11 +3754,6 @@ idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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'} and 'int' [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3774,6 +3799,7 @@ idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -3880,8 +3906,6 @@ idhelp.cpp:2070:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -3902,11 +3926,28 @@ 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ 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++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from hapglm.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from 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++) @@ -3930,7 +3971,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; @@ -3960,14 +4000,9 @@ 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp -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++) - | ~~^~~~~~~~~~~~~~~~~~ blox.cpp:569:41: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] 569 | if ( pB1>0 ) loglike1 += knownBA * log( pB1 ); | ~~~^~~~~~~ @@ -3992,11 +4027,45 @@ blox.cpp:489:10: note: 'pA1' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ +In file included from helper.h:24, + from zed.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from annot.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp +annot.cpp: In member function 'void Plink::annotateFile()': +annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 250 | if ( tokens.size() <= chr_column || + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 251 | tokens.size() <= bp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 260 | if ( tokens.size() <= pval_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 275 | if ( tokens.size() <= snp_column ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] + 300 | bool include = false; + | ^~~~~~~ In file included from 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] @@ -4026,11 +4095,6 @@ 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; | ^~~~~~~~~ @@ -4043,83 +4107,24 @@ 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; 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/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp -g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp In file included from Rconnection.h:42, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.h:42, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': -Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 203 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -Rconnection.cpp: At global scope: -Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ - | ^~~~~~~~~~~~~~ -Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': -Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 567 | if (host) free(host); host=0; - | ^~ -Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 567 | if (host) free(host); host=0; - | ^~~~ +g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from r.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] 47 | int bp; @@ -4152,6 +4157,54 @@ metaanal.cpp:300:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ +metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] + 253 | int pval_column = -1; + | ^~~~~~~~~~~ +metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 680 | for (int f=0; f=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +Rconnection.cpp: At global scope: +Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ + | ^~~~~~~~~~~~~~ +Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': +Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 567 | if (host) free(host); host=0; + | ^~ +Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 567 | if (host) free(host); host=0; + | ^~~~ +In file included from helper.h:24, + from r.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 203 | { name=""; fix_content(); } @@ -4175,18 +4228,6 @@ r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ -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