Diff of the two buildlogs: -- --- b1/build.log 2024-04-11 17:40:02.420241538 +0000 +++ b2/build.log 2024-04-11 17:42:13.598650154 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 11 05:36:20 -12 2024 -I: pbuilder-time-stamp: 1712856980 +I: Current time: Thu May 15 14:03:01 +14 2025 +I: pbuilder-time-stamp: 1747267381 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,54 +32,86 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/60753/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 May 15 00:03 /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/125916/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9ce9fbdd767647dfb69da0d0c47a386a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='60753' - PS1='# ' - PS2='> ' + INVOCATION_ID=a57af59b8c2d43c2b446ab5758a24c26 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=125916 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.pzKolIep/pbuilderrc_uhXP --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzKolIep/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.pzKolIep/pbuilderrc_PV2Y --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzKolIep/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/60753/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 14 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -148,7 +180,7 @@ Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] -Fetched 20.2 MB in 0s (66.5 MB/s) +Fetched 20.2 MB in 0s (74.0 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 ... 19874 files and directories currently installed.) @@ -287,7 +319,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -299,7 +335,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_clean - make -j8 clean + make -j21 clean make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' @@ -314,7 +350,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 - make -j8 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/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" FORCE_DYNAMIC=1 + make -j21 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/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" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp @@ -324,11 +360,61 @@ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 filters.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 locus.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 multi.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 assoc.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 epi.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 prephap.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 +In file included from informative.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from locus.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] + 80 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 102 | if ( col_length != tokens.size() ) + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ +informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 105 | for (int i=0;i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from options.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ -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 '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 '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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': -genome.cpp:99:15: warning: unused variable 'geno_nm' [-Wunused-variable] - 99 | int geno_nm = 0; - | ^~~~~~~ -genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] - 81 | double tothet = 0; - | ^~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::calcFst()': -genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] - 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); - | ^~ -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) - | ~~~~~~~~~~~~~~~~^~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] - 309 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 516 | if ( i == include.size() ) - | ~~^~~~~~~~~~~~~~~~~ -input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 521 | if ( i > include.size()) - | ~~^~~~~~~~~~~~~~~~ -input.cpp:545:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 545 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 579 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 595 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 611 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 631 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from plink.cpp:28: +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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'bool Plink::readClusterFile(bool)': -input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 787 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 817 | if (tokens.size() < 2+par::mult_clst) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 821 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] - 897 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 927 | for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 961 | else if ( ccount != tokens.size() ) - | ~~~~~~~^~~~~~~~~~~~~~~~ -input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 965 | if (tokens.size() < 2+par::mult_pheno) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from stats.cpp:30: +In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1043 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1064 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1208 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1232 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 1256 | if (tokens.size() < 2+par::mult_covar) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1261 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1335 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 58 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 90 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ +In file included from tinput.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ -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:1519:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i > msqrt(std::vector >&)': -stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] - 906 | const double eps = 1e-12; - | ^~~ +genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': +genome.cpp:99:15: warning: unused variable 'geno_nm' [-Wunused-variable] + 99 | int geno_nm = 0; + | ^~~~~~~ +genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] + 81 | double tothet = 0; + | ^~~~~~ +genome.cpp: In member function 'void Plink::calcFst()': +genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] + 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); + | ^~ 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 'unsigned int'} [-Wsign-compare] 193 | for (int t=0; t::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1792 | 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 'unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) @@ -619,75 +514,82 @@ helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 323 | for (int i=0; i::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] - 1531 | for (int i = 0; i < v.size(); i++) - | ~~^~~~~~~~~~ -input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2116 | for (int i=0; i >::size_type' {aka '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; + | ^~~ +In file included from prephap.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from multi.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': +helper.cpp:461:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 461 | for (int i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2172 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2200 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2210 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) +tinput.cpp:261:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ -input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2225 | for(int l=0; l < locus.size(); l++) +tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ -helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': -helper.cpp:461:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 461 | for (int i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 309 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 595 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ helper.cpp:611:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::pruneLD()': +genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1227 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 659 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 664 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 146 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] + 154 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int e=0;e > 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 'unsigned int'} [-Wsign-compare] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::updateAlleles()': -input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] - 2732 | bool success = false; - | ^~~~~~~ +tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from assoc.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 86 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 89 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) @@ -738,6 +671,9 @@ helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 1391 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from plink.cpp:28: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from stats.cpp:30: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] + 516 | if ( i == include.size() ) + | ~~^~~~~~~~~~~~~~~~~ +input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 521 | if ( i > include.size()) + | ~~^~~~~~~~~~~~~~~~ +epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] + 701 | int c=0; + | ^ +input.cpp:545:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 545 | if ( gn != 2 * include.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~~ +input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 579 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 595 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 611 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 631 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': +multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 295 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 304 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 357 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 372 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] + 191 | for (int i2=0; i2::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; + | ^~~~ +prephap.cpp: In member function 'void HaploPhase::readTagFile()': +prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 226 | if (len != tokens.size() - offset ) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 283 | for ( int i = allele ; i < tokens.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ +In file included from phase.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 91 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 520 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 526 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 553 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 412 | while ( index < tokens.size() ) + | ~~~~~~^~~~~~~~~~~~~~~ +prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 416 | if ( tokens[index].size() != len ) + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ +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 'unsigned int'} [-Wsign-compare] + 787 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 420 | if ( index == tokens.size() - 1 ) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; | ^ +mds.cpp:279:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 470 | for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2455 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2462 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2491 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2549 | for (int i=0; i&, std::vector&, std::vector >&)': +stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] + 458 | int m,l,iter,i,k; + | ^ helper.cpp: In member function 'void Plink::filterOnFemale()': helper.cpp:2568:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2568 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2606 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 817 | if (tokens.size() < 2+par::mult_clst) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 821 | for (int i0=0; i0 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2671 | for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2722 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2359 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 897 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2362 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2366 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ -helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2756 | for (int j=1; j, Individual*>&)': -helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 2935 | for (int i=0; i&)': -helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 2959 | if ( input.size() != P.nl_all ) - | ~~~~~~~~~~~~~^~~~~~~~~~~ -helper.cpp: In function 'std::map, std::set > readRange(std::string)': -helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] - 3097 | set * s; - | ^ -helper.cpp: In function 'void makeScaffold(Plink&)': -helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] - 3324 | int last = -1; - | ^~~~ -helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] - 3328 | int thisChromosome = P.locus[0]->chr; - | ^~~~~~~~~~~~~~ -helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] - 3329 | int nextChromosome; - | ^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 filters.cpp -helper.cpp: In member function 'std::string CArgs::value(std::string)': -helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] - 218 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'int CArgs::value_int(std::string)': -helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] - 231 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': -helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] - 243 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In member function 'double CArgs::value_double(std::string)': -helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] - 255 | error("Missing an argument for "+s); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -helper.cpp: In function 'int getInt(std::string, std::string)': -helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] - 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': -helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] - 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -helper.cpp: In function 'double getDouble(std::string, std::string)': -helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] - 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from 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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +stats.cpp: In function 'std::vector > msqrt(std::vector >&)': +stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] + 906 | const double eps = 1e-12; + | ^~~ +input.cpp:927:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 927 | for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 961 | else if ( ccount != tokens.size() ) + | ~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 965 | if (tokens.size() < 2+par::mult_pheno) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 95 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1043 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 123 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 163 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1064 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 198 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] + 1531 | for (int i = 0; i < v.size(); i++) + | ~~^~~~~~~~~~ +trio.cpp: In member function 'void Plink::parseTrios()': +trio.cpp:258:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 258 | for (int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~ +trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 272 | for (int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::makePhenotype()': +input.cpp:1208:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1208 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1232 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1256 | if (tokens.size() < 2+par::mult_covar) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1261 | for (int i0=0; i0 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 273 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 335 | for (int k=0; k < (*f)->kid.size() ;k++) + | ~~^~~~~~~~~~~~~~~~~~ +trio.cpp:342:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 342 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] 249 | double freq; | ^~~~ filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] 250 | int nm; | ^~ +trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 350 | for ( int k=0; k<(*f)->kid.size(); k++) + | ~^~~~~~~~~~~~~~~~~ +helper.cpp:2671:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2671 | for (int j=1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1335 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 591 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 739 | for ( int l = 0 ; l < locus.size() ; l++ ) - | ~~^~~~~~~~~~~~~~ -filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 762 | for ( int i = 0 ; i < sample.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1078 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1091 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1165 | for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from multi.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': -multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 295 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 304 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 357 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 372 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp -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 'unsigned int'} [-Wsign-compare] - 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] - 191 | for (int i2=0; i2::size_type' {aka '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 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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -cluster.cpp: In member function 'void Plink::buildCluster()': -cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 272 | for (int z=1; z<=qt.size(); z++) - | ~^~~~~~~~~~~ cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 452 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 611 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 511 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 373 | for (int i=0; i&)': +phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 472 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] + 678 | for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2722 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 469 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 474 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 492 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 504 | for (int c=0; c >::size_type' {aka 'unsigned int'} [-Wsign-compare] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ @@ -1038,30 +1092,92 @@ cluster.cpp:786:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 786 | for (int j=0;j >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +filters.cpp:739:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 739 | for ( int l = 0 ; l < locus.size() ; l++ ) + | ~~^~~~~~~~~~~~~~ +filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 762 | for ( int i = 0 ; i < sample.size() ; i++ ) + | ~~^~~~~~~~~~~~~~~ +assoc.cpp: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': +assoc.cpp:395:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 395 | for (int i=0; iprofileSNPs.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~ +phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::map, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1187 | if ( nh != hapmap.size() ) + | ~~~^~~~~~~~~~~~~~~~ +helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2756 | for (int j=1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1238 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1280 | for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 919 | for (int k=0;k::size_type' {aka 'unsigned int'} [-Wsign-compare] + 871 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1299 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] + 882 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 954 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 955 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 741 | for (int j=0; jselectedSNPs[l].size(); j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:975:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 975 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 976 | for (int j=i+1; j, Individual*>&)': +helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2935 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +trio.cpp:895:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 895 | for (int c=0; c::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j&)': +helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 2959 | if ( input.size() != P.nl_all ) + | ~~~~~~~~~~~~~^~~~~~~~~~~ +trio.cpp:931:13: warning: unused variable 'tmp' [-Wunused-variable] + 931 | int tmp = deleteSNPs(mendel_locus); + | ^~~ cluster.cpp:1041:40: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +trio.cpp:936:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 936 | for (int f=0;f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1049 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1107 | for (int i=0; i > >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 785 | for (int i=0;ipv_set.size();i++) + | ~^~~~~~~~~~~~~~~~~~ +assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 788 | for (int j=0;jpv_set[i].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1078 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1091 | for (int l=0; l >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1203 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1204 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) + | ~~^~~~~~~~~~~~~~ cluster.cpp: In function 'double groupAvgLink(std::vector >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1228 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1255 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 943 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ cluster.cpp: In function 'bool spec_clusters(Plink&, std::vector&, std::vector&)': cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1272 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1276 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1290 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1572 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1165 | for ( int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 1602 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1829 | for (int z=0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1843 | for (int z=0; z < new_pp.size(); z++) + | ~~^~~~~~~~~~~~~~~ +input.cpp:1745:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1792 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1661 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 86 | for (int j=0; j::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 520 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 526 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 553 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1038 | for (int f=0; f, std::set > readRange(std::string)': +helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] + 3097 | set * s; + | ^ +trio.cpp:1048:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1048 | for (int c=0; c&)': +phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1888 | for (int z = 0; z < h1.size(); z++) + | ~~^~~~~~~~~~~ +filters.cpp: In member function 'void Plink::thinSNPs()': +filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] + 1277 | int x = 0; + | ^ +In file included from plink.cpp:40: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1236 | for ( int k=0; kpm->kids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1245 | for ( int k=0; kpp->kids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': +input.cpp:2471:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2471 | for (int i=0; ichr; + | ^~~~~~~~~~~~~~ +helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] + 3329 | int nextChromosome; + | ^~~~~~~~~~~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] + 1536 | int best = 0 ; + | ^~~~ +input.cpp: In member function 'void Plink::updateAlleles()': +input.cpp:2732:12: warning: unused variable 'success' [-Wunused-variable] + 2732 | bool success = false; + | ^~~~~~~ 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 'unsigned int'} [-Wsign-compare] 2200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 80 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 102 | if ( col_length != tokens.size() ) - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ -informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 105 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from assoc.cpp:29: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 395 | for (int i=0; iprofileSNPs.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:741:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 741 | for (int j=0; jselectedSNPs[l].size(); j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 785 | for (int i=0;ipv_set.size();i++) - | ~^~~~~~~~~~~~~~~~~~ -assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 788 | for (int j=0;jpv_set[i].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] - 1536 | int best = 0 ; - | ^~~~ -In file included from /usr/include/c++/13/vector:67, - from helper.h:18: -In member function 'void std::_Bit_iterator_base::_M_incr(std::ptrdiff_t)', - inlined from 'std::_Bit_iterator::iterator& std::_Bit_iterator::operator+=(std::iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:340:14, - inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:362:16, - inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:355:24, - inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1051:23, - inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: -/usr/include/c++/13/bits/stl_bvector.h:212:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] - 212 | __n = __n % int(_S_word_bit); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1405:11: note: 'maxI' was declared here - 1405 | int maxI; - | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 epi.cpp -output.cpp: In member function 'void Plink::display_pairList()': -output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:7: note: 'i1' was declared here - 116 | int i1, i2; - | ^~ -output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] - 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:116:11: note: 'i2' was declared here - 116 | int i1, i2; - | ^~ -In file included from epi.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp -epi.cpp: In member function 'void Plink::calcEpistasis()': -epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 146 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] - 154 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int e=0;e::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: -/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, - inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: -/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] - 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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: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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': -assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] - 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) - | ^~ -assoc.cpp:1019:14: note: 'pvalue' was declared here - 1019 | double pvalue; - | ^~~~~~ -prephap.cpp: In member function 'void HaploPhase::readTagFile()': -prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 226 | if (len != tokens.size() - offset ) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 283 | for ( int i = allele ; i < tokens.size() ; i++ ) - | ~~^~~~~~~~~~~~~~~ -prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 412 | while ( index < tokens.size() ) - | ~~~~~~^~~~~~~~~~~~~~~ -prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 416 | if ( tokens[index].size() != len ) - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ -prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 420 | if ( index == tokens.size() - 1 ) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 470 | for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 560 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_indivReport()': -output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] - 69 | << setw(6) << genotype(*this,i1,l) << "\n"; - | ~~~~~~~~^~~~~~~~~~~~ -output.cpp:46:7: note: 'i1' was declared here - 46 | int i1; - | ^~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] - 91 | if ( feof(PED) ) - | ~~~~^~~~~ -input.cpp:60:10: note: 'PED' was declared here - 60 | FILE * PED; - | ^~~ -In file included from phase.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: -/usr/include/c++/13/ostream:223:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 223 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1385:22: note: 'mult_chisq' was declared here - 1385 | double mult_p, mult_chisq; - | ^~~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: -/usr/include/c++/13/ostream:223:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 223 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:14: note: 'dom_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: -/usr/include/c++/13/ostream:223:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 223 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:25: note: 'rec_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: -/usr/include/c++/13/ostream:223:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] - 223 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': -assoc.cpp:1430:36: note: 'gen_chisq' was declared here - 1430 | double dom_chisq, rec_chisq, gen_chisq; - | ^~~~~~~~~ -phase.cpp: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': -phase.cpp:373:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 373 | for (int i=0; i&)': -phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 472 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] - 678 | for (int z=0; z, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1187 | if ( nh != hapmap.size() ) - | ~~~^~~~~~~~~~~~~~~~ -phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1238 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1280 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1299 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) - | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp -phase.cpp: In member function 'void HaploPhase::prunePhase(int)': -phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1829 | for (int z=0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1843 | for (int z=0; z < new_pp.size(); z++) - | ~~^~~~~~~~~~~~~~~ -phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': -phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1888 | for (int z = 0; z < h1.size(); z++) - | ~~^~~~~~~~~~~ -In file included from trio.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -trio.cpp: In function 'void addPerson(Family*, Individual*)': -trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 91 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~ -trio.cpp: In member function 'void Plink::parseTrios()': -trio.cpp:258:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 258 | for (int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~ -trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 272 | for (int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~ -trio.cpp:335:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 335 | for (int k=0; k < (*f)->kid.size() ;k++) - | ~~^~~~~~~~~~~~~~~~~~ -trio.cpp:342:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 342 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 350 | for ( int k=0; k<(*f)->kid.size(); k++) - | ~^~~~~~~~~~~~~~~~~ -trio.cpp: In member function 'void Plink::checkMendel()': -trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 469 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 474 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 492 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 504 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 871 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 882 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 895 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 936 | for (int f=0;f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 943 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -trio.cpp:962:13: warning: unused variable 'tmp' [-Wunused-variable] - 962 | int tmp = deleteIndividuals(indel); - | ^~~ -trio.cpp: In member function 'void Plink::pseudoCaseControl()': -trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1038 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2359 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1048 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1236 | for ( int k=0; kpm->kids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1245 | for ( int k=0; kpp->kids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 +plink.cpp:2362:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2362 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 2366 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp -In file included from sets.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] + 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; + | ~~~^~~~~~~~~~~~~~~~~ +tdt.cpp:460:10: note: 'zt' was declared here + 460 | double zt; + | ^~ genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] 78 | } @@ -1682,6 +1586,26 @@ genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp +output.cpp: In member function 'void Plink::display_pairList()': +output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] + 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:7: note: 'i1' was declared here + 116 | int i1, i2; + | ^~ +output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] + 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " + | ~~~~~~~~^~~~~~~~~~~~ +output.cpp:116:11: note: 'i2' was declared here + 116 | int i1, i2; + | ^~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -1793,6 +1717,12 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 144 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ +mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': +mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': +mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1249 | for (int i=0; i >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 64 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.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 'unsigned int'} [-Wsign-compare] - 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': -mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1249 | for (int i=0; i Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': +assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] + 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) + | ^~ +assoc.cpp:1019:14: note: 'pvalue' was declared here + 1019 | double pvalue; + | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 In file included from helper.h:24, from gxe.cpp:20: @@ -1851,6 +1781,83 @@ 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp +In file included from /usr/include/c++/13/string:51, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from cluster.cpp:14: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: +/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, + inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: +/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] + 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/iostream:41, + from assoc.cpp:14: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: +/usr/include/c++/13/ostream:223:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 223 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1385:22: note: 'mult_chisq' was declared here + 1385 | double mult_p, mult_chisq; + | ^~~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: +/usr/include/c++/13/ostream:223:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 223 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:14: note: 'dom_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: +/usr/include/c++/13/ostream:223:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 223 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:25: note: 'rec_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: +/usr/include/c++/13/ostream:223:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] + 223 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': +assoc.cpp:1430:36: note: 'gen_chisq' was declared here + 1430 | double dom_chisq, rec_chisq, gen_chisq; + | ^~~~~~~~~ In file included from 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 'unsigned int'} [-Wsign-compare] @@ -1869,6 +1876,13 @@ merge.cpp:403:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 403 | for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] 426 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 842 | for (int i=0; i >&, Set&, Plink&)': genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; @@ -1894,14 +1911,12 @@ genepi.cpp:614:17: note: 'cancor1_pos' was declared here 614 | int cancor1_pos; | ^~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from hotel.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp 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) @@ -1909,12 +1924,24 @@ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 173 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from poo.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 85 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 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 'unsigned int'} [-Wsign-compare] @@ -1963,22 +1983,6 @@ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploTDT.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 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 93 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 328 | for (int c=0; c >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] 239 | double zt; | ^~ +In file included from haploTDT.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 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ -merge.cpp:943:8: note: 'write' was declared here - 943 | bool write; - | ^~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -2068,7 +2074,9 @@ qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] 639 | int tc = 0; | ^~ -In file included from parse.cpp:20: +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -2079,19 +2087,6 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -linear.cpp: In member function 'virtual void LinearModel::pruneY()': -linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 50 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 440 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 50 | for (int i=0; isecond; | ^~~~ @@ -2129,50 +2128,35 @@ bmerge.cpp:883:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 883 | for (int i=0; i, int>&)': +merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] + 1103 | if (write) + | ^~ +merge.cpp:943:8: note: 'write' was declared here + 943 | bool write; + | ^~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 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 '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 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] - 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 dcdflib.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 elf.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': -linear.cpp:96:5: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] - 96 | if (irow != icol) { - | ^~ -linear.cpp:75:9: note: 'icol' was declared here - 75 | int i,icol,irow,j,k,l,ll; - | ^~~~ -linear.cpp:96:5: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] - 96 | if (irow != icol) { - | ^~ -linear.cpp:75:14: note: 'irow' was declared here - 75 | int i,icol,irow,j,k,l,ll; - | ^~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 368 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': +dcdflib.cpp:1882:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 1882 | if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; + | ~~~~~~~~~~~~^~~~~~~~~~~ +dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': +dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; + | ~~~~~~^~~~~~~~~~~~~~ +dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': +dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; + | ~~~~~~^~~~~~~~~~~~~ +dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; + | ~~~~~~^~~~~~~~~~~~~~ +dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; + | ~~~~~~^~~~~~~~~~~~~~ +dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] + 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; + | ^~~ +dcdflib.cpp: In function 'double dlanor(double*)': +dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dcdflib.cpp: In function 'double dstrem(double*)': +dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': +dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from 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 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] + 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from model.cpp:17: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&)': +model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 132 | if ( include.size() != P->n ) + | ~~~~~~~~~~~~~~~^~~~~~~ +model.cpp: In member function 'void Model::buildDesignMatrix()': +model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 354 | for (int i=0; i< par::parameter_list.size(); i++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 367 | for ( int i = 0 ; i < X.size() ; i++) + | ~~^~~~~~~~~~ +model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'bool Model::checkVIF()': +model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] + 613 | double maxVIF = 0; + | ^~~~~~ In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:67, + from helper.h:18: +In member function 'void std::_Bit_iterator_base::_M_incr(std::ptrdiff_t)', + inlined from 'std::_Bit_iterator::iterator& std::_Bit_iterator::operator+=(std::iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:340:14, + inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:362:16, + inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:355:24, + inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1051:23, + inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: +/usr/include/c++/13/bits/stl_bvector.h:212:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] + 212 | __n = __n % int(_S_word_bit); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1405:11: note: 'maxI' was declared here + 1405 | int maxI; + | ^~~~ +In file included from helper.h:24, + from elf.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 673 | for (int i=0; i < plist.size(); i++) @@ -2238,6 +2330,26 @@ homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 861 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from segment.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) @@ -2254,38 +2366,50 @@ homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1441 | if ( (*pA)->match[i].size() >= maxlist ) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 493 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1461 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ -homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': -homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] - 2155 | homozygWindows[l] == 0; -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp -legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': -legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] - 203 | << start - last - 1 << " "; - | ~~~~~~^~~~~~ -legacy.cpp:35:7: note: 'last' was declared here - 35 | int last; - | ^~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp -In file included from model.cpp: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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from segment.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from model.cpp:17: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 609 | for (int l=0; l< original.size(); l++) + | ~^~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': +elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] + 654 | const double pthresh = 0.01; + | ^~~~~~~ +elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] + 655 | bool one_sided = true; + | ^~~~~~~~~ +elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] + 707 | int srange_cnt = 0; + | ^~~~~~~~~~ +elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] + 708 | bool inRange = false; + | ^~~~~~~ +elf.cpp: In member function 'void Plink::displayRareRange()': +elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 895 | for (int i = 0 ; i < tokens.size() ; i++) + | ~~^~~~~~~~~~~~~~~ +elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 939 | if ( tokens.size() != ncol ) + | ~~~~~~~~~~~~~~^~~~~~~ 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) @@ -2309,30 +2433,13 @@ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] 950 | int c=0; | ^ +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; segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i&)': -model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 132 | if ( include.size() != P->n ) - | ~~~~~~~~~~~~~~~^~~~~~~ -model.cpp: In member function 'void Model::buildDesignMatrix()': -model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 354 | for (int i=0; i< par::parameter_list.size(); i++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 367 | for ( int i = 0 ; i < X.size() ; i++) - | ~~^~~~~~~~~~ -model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 dcdflib.cpp -model.cpp: In member function 'bool Model::checkVIF()': -model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] - 613 | double maxVIF = 0; - | ^~~~~~ segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] 1855 | indivPair p = ic->first; @@ -2379,65 +2486,22 @@ 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ In file included from helper.h:24, - from logistic.cpp:20: + from glm.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i *xn)) goto S160; - | ~~~~~~~~~~~~^~~~~~~~~~~ -dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': -dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; - | ~~~~~~^~~~~~~~~~~~~~ -dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': -dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; - | ~~~~~~^~~~~~~~~~~~~ -dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; - | ~~~~~~^~~~~~~~~~~~~~ -dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; - | ~~~~~~^~~~~~~~~~~~~~ -dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] - 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; - | ^~~ -dcdflib.cpp: In function 'double dlanor(double*)': -dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dcdflib.cpp: In function 'double dstrem(double*)': -dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': -dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] 849 | error("Internal problem with QFAM model specification"); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from glm.cpp:19: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': +legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] + 203 | << start - last - 1 << " "; + | ~~~~~~^~~~~~ +legacy.cpp:35:7: note: 'last' was declared here + 35 | int last; + | ^~~~ 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 'unsigned int'} [-Wsign-compare] @@ -2456,9 +2520,13 @@ glm.cpp:423:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 423 | for (int c=0; c >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from dfam.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': -elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 493 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': -elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 609 | for (int l=0; l< original.size(); l++) - | ~^~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 76 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 86 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 96 | for ( int k=0; kkid.size(); k++) - | ~^~~~~~~~~~~~~~~~ -elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': -elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] - 654 | const double pthresh = 0.01; - | ^~~~~~~ -elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] - 655 | bool one_sided = true; - | ^~~~~~~~~ -elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] - 707 | int srange_cnt = 0; - | ^~~~~~~~~~ -elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] - 708 | bool inRange = false; - | ^~~~~~~ -dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 106 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 157 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] - 271 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 378 | for (int c=0; ckid.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~ -dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] - 218 | bool informative = false; - | ^~~~~~~~~~~ -dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 504 | for (int c=0; cperson.size(); c++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'void Plink::displayRareRange()': -elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 895 | for (int i = 0 ; i < tokens.size() ; i++) - | ~~^~~~~~~~~~~~~~~ -dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] - 151 | int totalInformative = 0; - | ^~~~~~~~~~~~~~~~ -elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 939 | if ( tokens.size() != ncol ) - | ~~~~~~~~~~~~~~^~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp -In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2618,12 +2612,16 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from dfam.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) @@ -2637,35 +2635,49 @@ linput.cpp:146:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 146 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 76 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 164 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 86 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 96 | for ( int k=0; kkid.size(); k++) + | ~^~~~~~~~~~~~~~~~ +dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 106 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 157 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] + 271 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 378 | for (int c=0; ckid.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] + 218 | bool informative = false; + | ^~~~~~~~~~~ +dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 504 | for (int c=0; cperson.size(); c++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] + 151 | int totalInformative = 0; + | ^~~~~~~~~~~~~~~~ linput.cpp:209:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 209 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': -sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] - 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request - | ^~~~~~~ -sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] - 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response - | ^~~~~~ -sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] - 81 | unsigned int i; // Loop counter - | ^ -sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] - 119 | int echoStringLen = 100; - | ^~~~~~~~~~~~~ In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': @@ -2688,33 +2700,52 @@ lookup.cpp:289:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 289 | for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from proxy.cpp:21: +sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': +sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] + 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request + | ^~~~~~~ +sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] + 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response + | ^~~~~~ +sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] + 81 | unsigned int i; // Loop counter + | ^ +sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] + 119 | int echoStringLen = 100; + | ^~~~~~~~~~~~~ +In file included from pdriver.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 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 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ pdriver.cpp: In member function 'void Plink::proxyWrapper()': pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] 266 | int similar = 0; | ^~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2727,6 +2758,7 @@ proxy.cpp:332:29: warning: comparison of integer expressions of different signedness: 'std::set::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2742,7 +2774,16 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.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) ) + | ~~~~^~~~~ +input.cpp:60:10: note: 'PED' was declared here + 60 | FILE * PED; + | ^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 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 'unsigned int'} [-Wsign-compare] @@ -2760,12 +2801,17 @@ haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp 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 'unsigned int'} [-Wsign-compare] @@ -2780,19 +2826,11 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::imputeAllHaplotypes()': haplohelper.cpp:104:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 487 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ +In file included from haplowindow.cpp:27: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 metaem.cpp +haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': +haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 183 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] 655 | for (int z=0; z::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 851 | ||alleles2.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ -haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': -haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 957 | if (mask1.size() != ns ||alleles1.size() != ns ) - | ~~~~~~~~~~~~~^~~~~ -haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 957 | if (mask1.size() != ns ||alleles1.size() != ns ) - | ~~~~~~~~~~~~~~~~^~~~~ -haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': -haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1225 | for (int z = 0; z < hap1[p1].size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) - | ~~~^~~~~~~~~~~~~~~~~ -haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++) - | ~~~^~~~~~~~~~~~~~~~~ -haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] - 1250 | int j=0; - | ^ -haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': -haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1419 | for( int z = 0; z < pp[i].size(); z++ ) - | ~~^~~~~~~~~~~~~~ -haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1477 | for( int z = 0; z < pp[i].size(); z++ ) - | ~~^~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from haplowindow.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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:27: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': -haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 183 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) @@ -2909,6 +2911,13 @@ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ +haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': +haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 957 | if (mask1.size() != ns ||alleles1.size() != ns ) + | ~~~~~~~~~~~~~^~~~~ +haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 957 | if (mask1.size() != ns ||alleles1.size() != ns ) + | ~~~~~~~~~~~~~~~~^~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 683 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 691 | for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 751 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 872 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] - 949 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 966 | for (int z2=0; z2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2957,7 +2954,37 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1225 | for (int z = 0; z < hap1[p1].size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) + | ~~~^~~~~~~~~~~~~~~~~ +haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++) + | ~~~^~~~~~~~~~~~~~~~~ +haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] + 1250 | int j=0; + | ^ +haplowindow.cpp: In member function 'void HaploWindow::reportPhase()': +haplowindow.cpp:949:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 949 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 966 | for (int z2=0; z2&)': +haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1419 | for( int z = 0; z < pp[i].size(); z++ ) + | ~~^~~~~~~~~~~~~~ +haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1477 | for( int z = 0; z < pp[i].size(); z++ ) + | ~~^~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2977,6 +3004,7 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) @@ -2988,8 +3016,6 @@ nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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: @@ -2997,6 +3023,11 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from em.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] @@ -3018,34 +3049,18 @@ clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 201 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -clumpld.cpp: In member function 'void clump_LD::clump()': -clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 368 | for (int i = 0; i < sp.size(); i++) - | ~~^~~~~~~~~~~ -clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 480 | if( l1 < P->locus.size()-1 ) - | ~~~^~~~~~~~~~~~~~~~~~~ -clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 520 | for (int f=1; f<=filename.size(); f++) - | ~^~~~~~~~~~~~~~~~~ -clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 611 | for (int f=1; f<=filename.size(); f++) - | ~^~~~~~~~~~~~~~~~~ -clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1097 | if( j < grouped_snps.size()-1) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from genoerr.cpp:27: +In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from genoerr.cpp:28: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 157 | for (int z=0; z::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 358 | for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 166 | for (int z=0; z::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:340:14, - inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:362:16, - inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:355:24, - inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1051:23, - inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: -/usr/include/c++/13/bits/stl_bvector.h:212:11: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] - 212 | __n = __n % int(_S_word_bit); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -proxy.cpp: In member function 'void Plink::performProxyTests(int)': -proxy.cpp:422:7: note: 'ref' was declared here - 422 | int ref; - | ^~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 impute.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 metaem.cpp +clumpld.cpp: In member function 'void clump_LD::clump()': +clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 368 | for (int i = 0; i < sp.size(); i++) + | ~~^~~~~~~~~~~ +In file included from genoerr.cpp:28: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] + 225 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 nlist.cpp +clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 480 | if( l1 < P->locus.size()-1 ) + | ~~~^~~~~~~~~~~~~~~~~~~ +genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 328 | for (int z2=0; z2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 520 | for (int f=1; f<=filename.size(); f++) + | ~^~~~~~~~~~~~~~~~~ +genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] + 358 | for (int z2=0; z2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 611 | for (int f=1; f<=filename.size(); f++) + | ~^~~~~~~~~~~~~~~~~ +clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1097 | if( j < grouped_snps.size()-1) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from impute.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp +elf.cpp: In member function 'void Plink::elfBaseline()': +elf.cpp:1159:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] + 1159 | ++(*p_cnt); + | ~^~~~~~~ +elf.cpp:1111:13: note: 'p_cnt' was declared here + 1111 | int * p_cnt; + | ^~~~~ +elf.cpp:1153:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] + 1153 | ++(*p_gcnt); + | ~^~~~~~~~ +elf.cpp:1112:13: note: 'p_gcnt' was declared here + 1112 | int * p_gcnt; + | ^~~~~~ In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3201,17 +3225,54 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from nlist.h:21, + from nlist.cpp:17: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': +nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': +nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 83 | for (int i=0; i NList::expandNumberList(std::vector&)': +nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 107 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 124 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 151 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 160 | for (int i=0; i > NList::tokenize(std::string)': +nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 189 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 239 | if ( s[i]== range_char && i == s.length()-1 ) + | ~~^~~~~~~~~~~~~~~ +nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] + 253 | else if ( i == s.length()-1 ) + | ~~^~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; @@ -3251,47 +3312,11 @@ profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 667 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': -nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': -nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 83 | for (int i=0; i NList::expandNumberList(std::vector&)': -nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 107 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 124 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 151 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 160 | for (int i=0; i > NList::tokenize(std::string)': -nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 189 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 239 | if ( s[i]== range_char && i == s.length()-1 ) - | ~~^~~~~~~~~~~~~~~ -nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] - 253 | else if ( i == s.length()-1 ) - | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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/reproducible-path/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 helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': @@ -3304,36 +3329,23 @@ options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] - 635 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 679 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1146 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 1211 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.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 'unsigned int'} [-Wsign-compare] + 635 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 393 | for (int g=0; g::size_type' {aka 'unsigned int'} [-Wsign-compare] 456 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] + 679 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g::size_type' {aka 'unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 1146 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 1211 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ @@ -3377,12 +3402,6 @@ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1118 | if ( mapping.size() != H->ns + H->nh ) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from gvar.cpp:15: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1129 | for (int i=0; i< lst.size(); i++) | ~^~~~~~~~~~~~ @@ -3418,7 +3437,18 @@ whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp +In file included from helper.h:24, + from gvar.cpp:15: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from cnv.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 125 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 556 | for (int i=0; i >::size_type' {aka '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; @@ -3476,6 +3499,7 @@ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ @@ -3497,16 +3521,42 @@ cnv.cpp:1103:43: warning: variable 'il' set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ +In file included from 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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] 412 | int nseg=0; | ^~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; | ^~~ +In file included from /usr/include/c++/13/vector:67, + from options.h:18: +In member function 'void std::_Bit_iterator_base::_M_incr(std::ptrdiff_t)', + inlined from 'std::_Bit_iterator::iterator& std::_Bit_iterator::operator+=(std::iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:340:14, + inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/13/bits/stl_bvector.h:362:16, + inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/13/bits/stl_bvector.h:355:24, + inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_bvector.h:1051:23, + inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:569:13: +/usr/include/c++/13/bits/stl_bvector.h:212:11: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] + 212 | __n = __n % int(_S_word_bit); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +proxy.cpp: In member function 'void Plink::performProxyTests(int)': +proxy.cpp:422:7: note: 'ref' was declared here + 422 | int ref; + | ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] 2013 | for (int c = 0 ; c < scaffold.size(); c++) @@ -3515,6 +3565,10 @@ cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] 2098 | noCovar == true; | ~~~~~~~~^~~~~~~ +greport.cpp: In member function 'void Plink::displayGeneReport()': +greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 78 | for (int i=0; ifirst; | ^ @@ -3527,30 +3581,6 @@ 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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from greport.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp -greport.cpp: In member function 'void Plink::displayGeneReport()': -greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 78 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 147 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ @@ -3563,12 +3593,23 @@ greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 169 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 240 | for (int l=0; l< ari->second.size(); l+=2) | ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3579,22 +3620,17 @@ qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 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 'unsigned int'} [-Wsign-compare] @@ -3706,6 +3742,12 @@ idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 678 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 727 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ @@ -3751,6 +3793,7 @@ idhelp.cpp:922:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 922 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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:950:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 950 | for ( int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1128 | for ( int k = 0; k < (*i0)->values.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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:1183:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1183 | for (int z=0; zvalues.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ @@ -3857,7 +3901,6 @@ idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) @@ -3891,6 +3934,7 @@ idhelp.cpp:2070:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -3911,29 +3955,25 @@ 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 '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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp 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 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) @@ -3947,14 +3987,20 @@ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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 +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/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 blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -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 blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3989,23 +4035,60 @@ blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ -In file included from helper.h:24, - from zed.cpp:19: +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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp +In file included from Rconnection.cpp:30: +Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': +Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 203 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': +Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 206 | { name=""; fix_content(); } + | ^~ +Rconnection.h: In member function 'char* Rstrings::stringAt(int)': +Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +Rconnection.cpp: At global scope: +Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ + | ^~~~~~~~~~~~~~ +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 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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp +In file included from dosage.cpp: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 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int j=1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 110 | for ( int q = 0 ; q < qthresh.size() ; q++) + | ~~^~~~~~~~~~~~~~~~ annot.cpp:149:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 149 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from dosage.cpp:23: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 110 | for ( int q = 0 ; q < qthresh.size() ; q++) - | ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 513 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -4131,6 +4176,12 @@ metaanal.cpp:300:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] 253 | int pval_column = -1; | ^~~~~~~~~~~ @@ -4143,12 +4194,6 @@ metaanal.cpp:680:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 680 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -4173,39 +4218,30 @@ r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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.cpp:30: -Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': -Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 203 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -Rconnection.cpp: At global scope: -Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ - | ^~~~~~~~~~~~~~ -g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/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 -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; - | ^~~~ +blox.cpp:510:10: warning: 'pA1' may be used uninitialized [-Wmaybe-uninitialized] + 510 | double D = pA1 - (pA*p1); + | ^ +blox.cpp:489:10: note: 'pA1' was declared here + 489 | double pA1,pA2,pB1,pB2; + | ^~~ +blox.cpp:503:10: warning: 'pA2' may be used uninitialized [-Wmaybe-uninitialized] + 503 | double pA = pA1 + pA2; + | ^~ +blox.cpp:489:14: note: 'pA2' was declared here + 489 | double pA1,pA2,pB1,pB2; + | ^~~ +blox.cpp:505:10: warning: 'pB1' may be used uninitialized [-Wmaybe-uninitialized] + 505 | double p1 = pA1 + pB1; + | ^~ +blox.cpp:489:18: note: 'pB1' was declared here + 489 | double pA1,pA2,pB1,pB2; + | ^~~ +blox.cpp:565:51: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] + 565 | double loglike1 = unknownDH * log( pA1*pB2 + pB1*pA2 ); + | ~~~^~~~ +blox.cpp:489:22: note: 'pB2' was declared here + 489 | double pA1,pA2,pB1,pB2; + | ^~~ r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ @@ -4289,12 +4325,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/125916/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/60753 and its subdirectories -I: Current time: Thu Apr 11 05:40:01 -12 2024 -I: pbuilder-time-stamp: 1712857201 +I: removing directory /srv/workspace/pbuilder/125916 and its subdirectories +I: Current time: Thu May 15 14:05:08 +14 2025 +I: pbuilder-time-stamp: 1747267508