Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/plink/plink_1.07+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/plink-1.07+dfsg-3o41dk543/plink_1.07+dfsg-3_amd64.buildinfo Get source package info: plink=1.07+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/plink/1.07+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-5 binutils=2.33.1-6 binutils-common=2.33.1-6 binutils-x86-64-linux-gnu=2.33.1-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-21 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.3 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.6.3-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.2.1-21 gcc=4:9.2.1-3.1 gcc-9=9.2.1-21 gcc-9-base=9.2.1-21 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.3-1 groff-base=1.22.4-4 gzip=1.9-3+b1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libarchive-zip-perl=1.67-1 libasan5=9.2.1-21 libatomic1=9.2.1-21 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.33.1-6 libblkid1=2.34-0.1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-7 libc-dev-bin=2.29-7 libc6=2.29-7 libc6-dev=2.29-7 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-21 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.10-9 libcrypt1=1:4.4.10-9 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.250 libdebhelper-perl=12.7.3 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.3-1 libgcc-9-dev=9.2.1-21 libgcc1=1:9.2.1-21 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.62.4-1 libgmp10=2:6.1.2+dfsg-4 libgomp1=9.2.1-21 libgpg-error0=1.36-7 libicu63=63.2-2 libisl22=0.22-2 libitm1=9.2.1-21 liblsan0=9.2.1-21 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncursesw6=6.1+20191019-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.2-1 libquadmath0=9.2.1-21 libseccomp2=2.4.2-2 libselinux1=3.0-1 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libstdc++-9-dev=9.2.1-21 libstdc++6=9.2.1-21 libsub-override-perl=0.09-2 libsystemd0=244-3 libtinfo6=6.1+20191019-1 libtool=2.4.6-11 libtsan0=9.2.1-21 libubsan1=9.2.1-21 libuchardet0=0.0.6-3 libudev1=244-3 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libxml2=2.9.4+dfsg1-8 linux-libc-dev=5.4.6-1 login=1:4.8-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-2 mawk=1.3.3-19 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-1 tar=1.30+dfsg-6+b1 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200101T211403Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d plink=1.07+dfsg-3 && mkdir -p /build/plink-MddXAD && dpkg-source --no-check -x /*.dsc /build/plink-MddXAD/plink-1.07+dfsg && chown -R builduser:builduser /build/plink-MddXAD" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/plink-MddXAD/plink-1.07+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1578209260" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/plink-MddXAD /tmp/plink-1.07+dfsg-3o41dk543 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200101T211403Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.2hF6CA6ubR as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.2hF6CA6ubR Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200101T211403Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200101T211403Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (873 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4507 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200101T211403Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.2hF6CA6ubR Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200101T211403Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1119 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.2hF6CA6ubR I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d plink=1.07+dfsg-3 && mkdir -p /build/plink-MddXAD && dpkg-source --no-check -x /*.dsc /build/plink-MddXAD/plink-1.07+dfsg && chown -R builduser:builduser /build/plink-MddXAD"' exec /tmp/mmdebstrap.2hF6CA6ubR Reading package lists... NOTICE: 'plink' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink.git Please use: git clone https://salsa.debian.org/med-team/plink.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 448 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main plink 1.07+dfsg-3 (dsc) [2079 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main plink 1.07+dfsg-3 (tar) [429 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main plink 1.07+dfsg-3 (diff) [16.8 kB] Fetched 448 kB in 0s (1256 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'plink_1.07+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting plink in /build/plink-MddXAD/plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/plink-MddXAD/plink-1.07+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1578209260" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.2hF6CA6ubR dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_auto_clean make -j4 clean make[2]: Entering directory '/build/plink-MddXAD/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -j4 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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/plink-MddXAD/plink-1.07+dfsg' g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 input.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 binput.cpp In file included from options.cpp:16: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from binput.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function ‘void Plink::readBinData()’: binput.cpp:126:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 126 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 176 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 186 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | while (s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 339 | while (s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 351 | while (c<7 && s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ In file included from input.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function ‘void Plink::readData()’: input.cpp:516:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 516 | if ( i == include.size() ) | ~~^~~~~~~~~~~~~~~~~ input.cpp:521:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 521 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 545 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 579 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 595 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 611 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 631 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 695 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function ‘bool Plink::readClusterFile(bool)’: input.cpp:787:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 787 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ input.cpp:821:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 821 | for (int i0=0; i0::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 897 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 927 | for ( int i=2; i >::size_type’ {aka ‘long 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 ‘long unsigned int’} and ‘int’ [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1037 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1043 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1064 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1208 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1232 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1256 | if (tokens.size() < 2+par::mult_covar) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1261:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1261 | for (int i0=0; i0::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1335 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1519:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1519 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1538 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1572 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1599 | else if (tokens.size() != par::plist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1602 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1745 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1764 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1792 | for (int i=0; i&, std::vector&, int&)’: input.cpp:2116:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2116 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2172 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2200 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2210 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2225 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ input.cpp: In member function ‘void Plink::readFamFile(std::string)’: input.cpp:2389:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2389 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2397 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2419 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2453 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2471 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 196 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2106 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2359 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2362 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2366 | for (int l=0; l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function ‘void Plink::readTransposedData()’: tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 161 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 246 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 256 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 271 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 309 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 591 | if ( c > sample.size()) | ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 603 | if ( gn != 2 * sample.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from genome.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function ‘void Plink::calcStratifiedAlleleFreqs()’: genome.cpp:99:8: 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 ); | ^~ 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:1067:23: 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 ‘long unsigned int’} [-Wsign-compare] 1227 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function ‘std::string display(std::vector >&)’: helper.cpp:58:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 58 | for (int i=0; i >&)’: helper.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 66 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ helper.cpp:79:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 79 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 90 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ helper.cpp: In function ‘void display(std::vector&)’: helper.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ helper.cpp: In member function ‘void CArgs::fromPriorLog(std::string)’: helper.cpp:193:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 193 | for (int t=0; t > CArgs::value(std::string, int)’: helper.cpp:267:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) | ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); | ~~~~~~~~~^~~~ helper.cpp: In function ‘std::vector > parse2str(std::string)’: helper.cpp:306:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 306 | for (int i=0 ; i < s.length() ; i++) | ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 307 | if (s[i] == ',' || i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ helper.cpp:309:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 309 | if (i == s.length()-1) t += s[i]; | ~~^~~~~~~~~~~~~~~ helper.cpp: In function ‘std::vector parse2int(std::string)’: helper.cpp:323:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 323 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 461 | for (int i=1; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 595 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 611 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 659 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 664 | for (int i=0;i > listPossibleHaplotypes(Plink&, std::vector)’: helper.cpp:709:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 709 | while(h >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 729 | for (int h=0; h::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 775 | for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)’: helper.cpp:795:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ helper.cpp: In function ‘std::string chromosomeName(int)’: helper.cpp:952:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function ‘int getMarkerChromosome(Plink&, std::string)’: helper.cpp:959:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 959 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 966 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 973 | for (int l=0;l getChromosomeMarkerRange(Plink&, int)’: helper.cpp:989:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 989 | for (int i=0;i getChromosomeRange(Plink&)’: helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1040 | for (int i=0;i >)’: helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1172 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1264 | if (sample[i]->fid.length() > par::pp_maxfid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1267 | if (sample[i]->iid.length() > par::pp_maxiid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1273 | if (locus[l]->name.length() > par::pp_maxsnp) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp: In function ‘std::vector vif_prune(std::vector >, double, std::vector&)’: helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1389 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1391 | for (int j=0; j&)’: helper.cpp:2204:12: warning: unused variable ‘i’ [-Wunused-variable] 2204 | int i = 0; | ^ helper.cpp: In member function ‘void Plink::filterOnCovariate()’: helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2455 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2462 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2491 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2510 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2530 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2549 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2568 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2587 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2606 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2638 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2671 | for (int j=1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2722 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2756 | for (int j=1; j, Individual*>&)’: helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2935 | for (int i=0; i&)’: helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~ 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:378:48: 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:391:48: 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:404:48: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from filters.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from stats.cpp:30: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function ‘void Plink::filterSNPs()’: filters.cpp:95:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 123 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 155 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 198 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 273 | 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; | ^ filters.cpp:591:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 591 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 611 | for (int i=0; i > msqrt(std::vector >&)’: stats.cpp:906:16: warning: unused variable ‘eps’ [-Wunused-variable] 906 | const double eps = 1e-12; | ^~~ filters.cpp:739:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 739 | for ( int l = 0 ; l < locus.size() ; l++ ) | ~~^~~~~~~~~~~~~~ filters.cpp:762:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 762 | for ( int i = 0 ; i < sample.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ stats.cpp: In function ‘int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)’: stats.cpp:1477:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1477 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1483 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1515 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1521 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp: In function ‘matrix_t vec2diag(vector_t&)’: stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1531 | for (int i = 0; i < v.size(); i++) | ~~^~~~~~~~~~ filters.cpp:1078:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1078 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1091 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1143 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1165 | for ( int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from multi.cpp:16: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function ‘std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)’: multi.cpp:295:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 295 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 357 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 372 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function ‘void Plink::buildCluster()’: cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ cluster.cpp:452:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 452 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 511 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 626 | for ( int i = 4; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 651 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 784 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 786 | for (int j=0;j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 919 | for (int k=0;k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 954 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 955 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 975 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 976 | for (int j=i+1; j::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1038:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1038 | for(int j=0;j >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ cluster.cpp:1049:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1049 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1050 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1060 | for (int j1=0; j1 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1061 | for (int j2=0; j2 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1107 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1110 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1133 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1163 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1169 | for (int i=0; i >&, std::vector&, std::vector&)’: cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1203 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1204 | for (int j=0; j >&, std::vector&, std::vector&)’: cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1228 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1229 | for (int j=0; j&, std::vector&)’: cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1254 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1255 | for (int j=0; j&, std::vector&)’: cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1272 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1276 | for (int j=0; j >&, std::vector&, std::vector&)’: cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1290 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1291 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1661 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1664 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function ‘void Plink::generateMDS()’: mds.cpp:190:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 190 | for (int i1=0; i1::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 191 | for (int i2=0; i2::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 279 | if ( elist.size() != par::cluster_mds_dim ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ mds.cpp:242:8: warning: unused variable ‘flag’ [-Wunused-variable] 242 | bool flag = svd(D,eigenvalue,eigenvector); | ^~~~ In file included from output.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function ‘void Plink::displayGenomePV()’: output.cpp:84:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 84 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int k=0; k::iterator loc1 = locus.begin()+m1; | ^~~~ output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable] 403 | vector::iterator loc2 = locus.begin()+m2; | ^~~~ output.cpp: In member function ‘void Plink::extractExcludeSet(bool)’: output.cpp:520:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 520 | for (int s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 526 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 553 | for (int l=0; l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2200 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2322 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2367 | for (int i=0; i < setname.size();i++) | ~~^~~~~~~~~~~~~~~~ output.cpp:2380:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2380 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2409 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2412 | for (int l=0; l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function ‘int Plink::readInformative()’: informative.cpp:80:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 105 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 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 ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 395 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 741 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 788 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ 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 epi.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function ‘void Plink::calcEpistasis()’: epi.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | for (int e=0;e::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 154 | for (int e=0;e::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 161 | for (int e=0;e Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)’: assoc.cpp:1109:61: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1109 | pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); | ~~~~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from prephap.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 226 | if (len != tokens.size() - offset ) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ prephap.cpp:283:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 283 | for ( int i = allele ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ prephap.cpp:412:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 412 | while ( index < tokens.size() ) | ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:34: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 416 | if ( tokens[index].size() != len ) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 470 | for (int s=0;s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 533 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 560 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 373 | for (int i=0; i&)’: phase.cpp:472:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 472 | while (h::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 678 | for (int z=0; z, int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1238 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1280 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1299 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) | ~~^~~~~~~~~~~~~~ phase.cpp: In member function ‘void HaploPhase::prunePhase(int)’: phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1829 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1843 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ phase.cpp: In member function ‘double HaploPhase::dosage(int, std::set&)’: phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ In file included from trio.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function ‘void addPerson(Family*, Individual*)’: trio.cpp:91:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 91 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~ trio.cpp: In member function ‘void Plink::parseTrios()’: trio.cpp:258:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 258 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:272:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 272 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:335:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 335 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 342 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp:350:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 350 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function ‘void Plink::checkMendel()’: trio.cpp:469:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 469 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 474 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 492 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 504 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 871 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 882 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 895 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 936 | for (int f=0;f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 943 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:6: warning: unused variable ‘tmp’ [-Wunused-variable] 962 | int tmp = deleteIndividuals(indel); | ^~~ trio.cpp: In member function ‘void Plink::pseudoCaseControl()’: trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1038 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1048 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1236 | for ( int k=0; kpm->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 tdt.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ tdt.cpp: In member function ‘void Plink::perm_testTDT(Perm&)’: tdt.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 81 | for (int i=0; iperson.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:16: warning: unused variable ‘person’ [-Wunused-variable] 96 | Individual * person = klist[k]->person[i]; | ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | for (int c=0; c < fam->kid.size(); c++) | ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 234 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 412 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 415 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ tdt.cpp: In member function ‘std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)’: tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 522 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 557 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 668 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 776 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function ‘void Plink::perm_sharingIBSTest(Perm&)’: sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int l=0; l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function ‘double C(int, double, double)’: genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] 78 | } | ^ genepi.cpp: In function ‘long double pillai(int, int, int, double)’: genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] 169 | } | ^ genepi.cpp: In member function ‘void Plink::driverSCREEPI()’: genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 334 | for (int s=0; s >&, Set&, Plink&)’: genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 489 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 497 | for (int l=0; l >&, Set&, Plink&)’: genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1025 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1033 | for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)’: genepi.cpp:1198:8: warning: unused variable ‘casewise_deletion’ [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 perm.cpp In file included from sets.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 37 | for(int s=0;s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 52 | for(int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 59 | else if (par::set_min > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 62 | if (par::set_max==-1 || par::set_max > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function ‘void Set::pruneSets(Plink&)’: sets.cpp:99:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 99 | for(int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 176 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 216 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function ‘void Set::makeLDSets()’: sets.cpp:317:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 323 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:329:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 329 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 332 | for (int k=j+1; k < snpset[i].size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 370 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function ‘void Set::initialiseSetMapping()’: sets.cpp:412:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 412 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function ‘void Set::empiricalSetPValues()’: sets.cpp:618:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 618 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 619 | for (int j=0;j > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 631 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 632 | for (int j=0;j > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 642 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 643 | for (int j=0;j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 703 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 713 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 905 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 975 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1042 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function ‘void Perm::permuteInCluster()’: perm.cpp:144:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 145 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 187 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 199 | for(int i=0; i&, std::vector&)’: perm.cpp:273:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ genepi.cpp: In function ‘void CCA_logit(bool, std::vector >&, Set&, Plink&)’: genepi.cpp:855:84: warning: ‘cancor1_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 855 | gene2[i] += (-1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; | ^ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 perm.h:17, from mh.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function ‘std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)’: mh.cpp:747:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)’: mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1249 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function ‘void Perm::preGeneDrop()’: genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (int i=0; i&, std::vector&, std::vector&, std::map&)’: genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from merge.cpp:22: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ merge.cpp: In member function ‘void Plink::mergeData()’: merge.cpp:333:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 333 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 377 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 395 | for (int l=0;l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 403 | for (int l=0;l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 426 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 722 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 733 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 784 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 830 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 842 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ hotel.cpp: In member function ‘void Plink::perm_testHotel(Perm&)’: hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 77 | if (!sample[i]->missing) | ^ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 173 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function ‘void Plink::multcomp(std::vector&, std::string)’: multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 131 | for (int i=0; i, int>&)’: merge.cpp:1103:3: warning: ‘write’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1103 | if (write) | ^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from haploCC.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)’: haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 62 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 79 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 93 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable ‘p’ [-Wunused-variable] 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); | ^ haploCC.cpp: In member function ‘void HaploPhase::haplotypicWeightedCC()’: haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 357 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 375 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:28: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 haploTDT.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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 ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function ‘void Plink::perm_testTDT_POO(Perm&)’: poo.cpp:93:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 93 | for (int f=0; f > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 195 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 198 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp: In member function ‘std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)’: poo.cpp:293:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 293 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 328 | for (int c=0; c >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function ‘void Plink::webcheck(CArgs&)’: webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 117 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 130 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 180 | if ( i < tokens.size() - 1) | ~~^~~~~~~~~~~~~~~~~~~ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 218 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function ‘void scoreBetween(Plink&, int)’: qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 97 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ qfam.cpp: In member function ‘void Plink::perm_testQTDT(Perm&)’: qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | for (int i=0; i < family.size(); i++) | ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 315 | for (int f = 0 ; f < family.size() ; f++) | ~~^~~~~~~~~~~~~~~ qfam.cpp: In member function ‘vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)’: qfam.cpp:505:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 648 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 657 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function ‘virtual void LinearModel::pruneY()’: linear.cpp:50:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 50 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function ‘void Plink::mergeBinaryData()’: bmerge.cpp:90:16: warning: variable ‘inc’ set but not used [-Wunused-but-set-variable] 90 | long int inc; | ^~~ bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 357 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 390 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 409 | for (int l=0;l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 417 | for (int l=0;l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | for (int i=0; isecond; | ^~~~ bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 697 | while (s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 839 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 871 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 883 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In function ‘void gaussj(matrix_t&, matrix_t&)’: linear.cpp:100:13: warning: ‘irow’ may be used uninitialized in this function [-Wmaybe-uninitialized] 100 | indxr[i]=irow; linear.cpp:108:7: warning: ‘icol’ may be used uninitialized in this function [-Wmaybe-uninitialized] 108 | if (ll != icol) { | ^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 mishap.cpp:17: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 helper.h:24, from legacy.cpp:22: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function ‘void Plink::calcRegression(int)’: legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 368 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 377 | for (int i=0;i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 381 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 384 | for (int j=0;j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 390 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 395 | for (int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 415 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 424 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 460 | for (int j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 461 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 462 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 467 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 480 | for (int i=0; ibp - locus[last]->bp ) / 1000.0 | ^ In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function ‘void displayPoolVerbose(Plink&, Pool*, std::ofstream&)’: homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 673 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 695 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 722 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 756 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 773 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:861:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 861 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp: In member function ‘void Plink::summariseHomoRuns()’: homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1178:31: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1178 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1331 | for (int i=0; i< (*pA)->segs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1437 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1441 | if ( (*pA)->match[i].size() >= maxlist ) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1461 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function ‘void Plink::findHomoWindow(Individual*, std::ofstream&)’: homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from helper.h:24, from segment.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function ‘void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)’: segment.cpp:871:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) | ^~ segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 875 | SIBS << setw(10) << original[l] << " " | ^~~~ segment.cpp: In member function ‘void Plink::testGenomeIBDByCovariate(Perm&)’: segment.cpp:954:15: warning: unused variable ‘p1’ [-Wunused-variable] 954 | Individual * p1 = sample[i1]; | ^~ segment.cpp:955:15: warning: unused variable ‘p2’ [-Wunused-variable] 955 | Individual * p2 = sample[i2]; | ^~ segment.cpp:1027:19: warning: unused variable ‘p1’ [-Wunused-variable] 1027 | Individual * p1 = sample[i1]; | ^~ segment.cpp:1028:19: warning: unused variable ‘p2’ [-Wunused-variable] 1028 | Individual * p2 = sample[i2]; | ^~ segment.cpp:950:7: warning: unused variable ‘c’ [-Wunused-variable] 950 | int c=0; | ^ segment.cpp: In member function ‘void Plink::summaryIBD()’: segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1529 | for (int i=0;ifirst; | ^ segment.cpp: In member function ‘void Plink::displaySegmentsLong()’: segment.cpp:2003:12: warning: unused variable ‘nseg’ [-Wunused-variable] 2003 | int nseg = smap.size(); | ^~~~ segment.cpp: In member function ‘void Plink::displaySegmentsBED()’: segment.cpp:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2378 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2380 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2382 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2412 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2414 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2416 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2443 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2445 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2447 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2474 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2476 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ In file included from model.cpp:15: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from model.cpp:17: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i&)’: model.cpp:132:23: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 132 | if ( include.size() != P->n ) | ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function ‘void Model::buildDesignMatrix()’: model.cpp:354:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 354 | for (int i=0; i< par::parameter_list.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | for ( int i = 0 ; i < X.size() ; i++) | ~~^~~~~~~~~~ model.cpp:374:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function ‘bool Model::checkVIF()’: model.cpp:613:10: warning: unused variable ‘maxVIF’ [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ 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"); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 helper.h:24, from logistic.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ logistic.cpp: In member function ‘virtual void LogisticModel::pruneY()’: logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 66 | for (int i=0; i *xn)) goto S160; | ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.cpp: In function ‘void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)’: dcdflib.cpp:3544:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp: In function ‘void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)’: dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp:6088:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; | ~~~~~~^~~~~~~~~~~~~ dcdflib.cpp:6112:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6153:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6020:56: warning: variable ‘qok’ set but not used [-Wunused-but-set-variable] 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; | ^~~ dcdflib.cpp: In function ‘double dlanor(double*)’: dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp: In function ‘double dstrem(double*)’: dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp: In function ‘void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)’: dcdflib.cpp:6996:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 glm.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from glm.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 294 | for (int h=1; h < whap->current->group.size(); h++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 344 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 355 | for (int c=0; c::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 423 | for (int c=0; c >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In function ‘void displayScoresRegion(std::ofstream&, RCount&)’: elf.cpp:493:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 493 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function ‘void Plink::permTestRareDistribution(Perm&)’: elf.cpp:609:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 609 | for (int l=0; l< original.size(); l++) | ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function ‘vector_t Plink::testRareDistribution(Perm&, bool, std::map&)’: elf.cpp:654:16: warning: unused variable ‘pthresh’ [-Wunused-variable] 654 | const double pthresh = 0.01; | ^~~~~~~ elf.cpp:655:8: warning: unused variable ‘one_sided’ [-Wunused-variable] 655 | bool one_sided = true; | ^~~~~~~~~ elf.cpp:707:7: warning: unused variable ‘srange_cnt’ [-Wunused-variable] 707 | int srange_cnt = 0; | ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable ‘inRange’ [-Wunused-variable] 708 | bool inRange = false; | ^~~~~~~ elf.cpp: In member function ‘void Plink::displayRareRange()’: elf.cpp:895:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 895 | for (int i = 0 ; i < tokens.size() ; i++) | ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ glm.cpp:610:28: warning: ‘df’ may be used uninitialized in this function [-Wmaybe-uninitialized] 610 | double pvalue = chiprobP(chisq,df); | ~~~~~~~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 dfam.cpp In file included from dfam.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function ‘std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)’: dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:106:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 106 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 271 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 378 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:9: warning: unused variable ‘informative’ [-Wunused-variable] 218 | bool informative = false; | ^~~~~~~~~~~ dfam.cpp:504:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 504 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable ‘totalInformative’ [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 fisher.cpp elf.cpp: In member function ‘bool RCount::addSNP(int)’: elf.cpp:374:10: warning: ‘wt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 374 | double wt; | ^~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ fisher.cpp: In function ‘void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)’: fisher.cpp:261:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 261 | prterr(1, "NROW must be less than or equal to LDTABL."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:267:14: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 267 | prterr(2, "All elements of TABLE must be positive."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 272 | prterr(3, "All elements of TABLE are zero.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 273 | "PRT and PRE are set to missing values."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function ‘void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)’: fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 448 | prterr(1, "NROW must be less than or equal to LDTABL."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 450 | prterr(4, "NCOL must be at least 2"); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:449:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 449 | if (*ncol <= 1) | ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 453 | for (i = 1; i <= *ldkey << 1; ++i) { | ^~~ fisher.cpp:501:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 501 | prterr(2, "All elements of TABLE must be positive."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 508 | prterr(3, "All elements of TABLE are zero.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 509 | "PRT and PRE are set to missing values."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 559 | prterr(5, "The hash table key cannot be computed because " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | "the largest key\n" | ~~~~~~~~~~~~~~~~~~~ 561 | "is larger than the largest representable int.\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | "The algorithm cannot proceed.\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | "Reduce the workspace size, or use `exact = FALSE'."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 750 | prterr(6, "LDKEY is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function ‘void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)’: fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1538 | prterr(6, "LDKEY is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1539 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:1554:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1554 | prterr(7, "LDSTP is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1555 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1596 | prterr(7, "LDSTP is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1597 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function ‘int iwork(int, int*, int, int)’: fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2001 | prterr(40, "Out of workspace."); | ^~~~~~~~~~~~~~~~~~~ fisher.cpp: In function ‘void isort(int*, int*)’: 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 -fdebug-prefix-map=/build/plink-MddXAD/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 linput.cpp:25: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function ‘void Plink::readDataLongFormat()’: linput.cpp:68:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ elf.cpp: In member function ‘void Plink::elfBaseline()’: elf.cpp:1154:8: warning: ‘p_gcnt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1154 | ++(*p_gcnt); | ^~~~~~~~~~~ elf.cpp:1165:5: warning: ‘p_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1165 | ++(*p_cnt); | ^~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 128 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ linput.cpp:164:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 164 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 200 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 209 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function ‘std::vector > socketConnection(Plink*, std::string, int, std::string)’: sockets.cpp:78:24: warning: unused variable ‘out_buf’ [-Wunused-variable] 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request | ^~~~~~~ sockets.cpp:79:24: warning: unused variable ‘in_buf’ [-Wunused-variable] 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response | ^~~~~~ sockets.cpp:81:24: warning: unused variable ‘i’ [-Wunused-variable] 81 | unsigned int i; // Loop counter | ^ sockets.cpp:119:7: warning: unused variable ‘echoStringLen’ [-Wunused-variable] 119 | int echoStringLen = 100; | ^~~~~~~~~~~~~ In file included from helper.h:24, from lookup.cpp:18: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function ‘void Plink::lookup()’: lookup.cpp:206:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 206 | for (int i=25; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 272 | for (int i=25; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 289 | for (int i=25; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 314 | for (int i=1; i::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:854:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 pdriver.cpp proxy.cpp:1332:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1401 | for (int c1 = 0; c1 < collection.size() ; c1++ ) | ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:12: warning: unused variable ‘t1’ [-Wunused-variable] 1448 | int t1=0; | ^~ proxy.cpp:169:10: warning: unused variable ‘s’ [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from pdriver.cpp:16: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploQTL.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)’: haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 83 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from haplohelper.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 104 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 134 | for (int l=0; l < actual_map.size(); l++) | ~~^~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function ‘std::vector > HaploPhase::returnHaplotypes(std::vector&)’: haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 297 | for (int h=0; h >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 337 | for (int h=0; h::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 396 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 413 | for (int z2=0; z2::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 487 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function ‘vector_t HaploPhase::imputeGenotype(int, int)’: haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 655 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 754 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 802 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare] 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) | ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long 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:1419:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1419 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1477 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ haplohelper.cpp: In member function ‘void HaploPhase::verboseDisplayWindows(int, bool)’: haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:939:58: warning: ‘ref’ may be used uninitialized in this function [-Wmaybe-uninitialized] 939 | haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " "; | ^ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 haplowindow.cpp:23: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function ‘void HaploWindow::enumerateHaplotypes(intvec_t&)’: haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 183 | while (h::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function ‘void HaploWindow::performEM()’: haplowindow.cpp:683:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 683 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 691 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 751 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 791 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 798 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 868 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 872 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 949 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 966 | for (int z2=0; z2 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i clump_LD::read_assoc_file(std::string)’: clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 92 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 128 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 137 | for ( int f=0; f >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 173 | if ( tokens.size() <= snp_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ nonfounderphasing.cpp: In member function ‘void HaploPhase::phaseAndScoreNonfounder(int)’: nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) | ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable ‘pcnt’ [-Wunused-variable] 360 | int pcnt=1; | ^~~~ nonfounderphasing.cpp: In member function ‘void HaploPhase::transmissionCount(int, std::map&)’: nonfounderphasing.cpp:715:14: warning: unused variable ‘posterior’ [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ clumpld.cpp: In member function ‘void clump_LD::clump()’: clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) | ~~^~~~~~~~~~~ clumpld.cpp:480:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 480 | if( l1 < P->locus.size()-1 ) | ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 189 | for( int a = 0; a < posshap1.size(); a++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 190 | for( int b = 0; b < posshap2.size(); b++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 225 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 315 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 328 | for (int z2=0; z2::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 347 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 358 | for (int z2=0; z2 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from em.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 97 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 106 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 128 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 162 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 166 | for (int z=0; z >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ parse.cpp: In function ‘void setOptions(CArgs&)’: parse.cpp:80:6: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without 80 | void setOptions(CArgs & a) | ^~~~~~~~~~ In file included from impute.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 105 | for (int z=0; z::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function ‘void HaploPhase::mainImputation()’: impute.cpp:263:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ In file included from metaem.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’: genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 27 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ profile.cpp: In member function ‘void Plink::scoreIndividuals()’: profile.cpp:303:12: warning: unused variable ‘OLD_assoc_glm_without_main_snp’ [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ profile.cpp:304:12: warning: unused variable ‘OLD_clist’ [-Wunused-variable] 304 | bool OLD_clist = par::clist; | ^~~~~~~~~ profile.cpp:350:14: warning: unused variable ‘statistic’ [-Wunused-variable] 350 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ profile.cpp:351:14: warning: unused variable ‘pvalue’ [-Wunused-variable] 351 | double pvalue = pval[ pval.size()-1 ]; | ^~~~~~ profile.cpp:352:14: warning: unused variable ‘beta’ [-Wunused-variable] 352 | double beta = b[ b.size()-1 ]; | ^~~~ profile.cpp:390:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 390 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 402 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function ‘void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)’: profile.cpp:480:9: warning: unused variable ‘a1’ [-Wunused-variable] 480 | bool a1 = i2->second; | ^~ profile.cpp:525:9: warning: variable ‘sawNamedAllele’ set but not used [-Wunused-but-set-variable] 525 | bool sawNamedAllele = false; | ^~~~~~~~~~~~~~ profile.cpp:629:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)’: profile.cpp:667:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 667 | for (int l=0; l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function ‘std::vector NList::deparseNumberList(std::string)’: nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)’: nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 83 | for (int i=0; i NList::expandNumberList(std::vector&)’: nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 107 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 124 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 151 | for (int i=0; i::size_type’ {aka ‘long 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 ‘long unsigned int’} [-Wsign-compare] 189 | for (int i=0; i::size_type’ {aka ‘long 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 ‘long unsigned int’} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ In file included from helper.h:24, from whap.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 393 | for (int g=0; g::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 454 | for (int h=0; h::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 456 | for (int h=0; h >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 508 | for ( int g=0; g >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp: In member function ‘void Chap::build(ChapModel&)’: whap.cpp:962:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 962 | for (int h=0; h >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 986 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1015 | for (int i=0; i< tok.size(); i++) | ~^~~~~~~~~~~~ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1048 | for ( int i = 0 ; i < tok.size() ; i++ ) | ~~^~~~~~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: ‘std::map, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1118 | if ( mapping.size() != H->ns + H->nh ) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1129 | for (int i=0; i< lst.size(); i++) | ~^~~~~~~~~~~~ whap.cpp:1142:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1142 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1162 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1197 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1231 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1290 | for (int g=0; g< model.group.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~ whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1326 | for (int c=0; c < P->conditioner.size(); c++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1334 | for (int l=0; l&, ChapModel&)’: whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1389 | for (int l=0;l >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1425 | for (int h=0; h < m.group.size(); h++) | ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from helper.h:24, from simul.cpp:16: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function ‘vector_t instanceSNP(SimParameters&)’: simul.cpp:172:10: warning: unused variable ‘gh_11_12’ [-Wunused-variable] 172 | double gh_11_12 = h11*h12; | ^~~~~~~~ simul.cpp: In member function ‘void Plink::simulateSNPs()’: simul.cpp:635:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 635 | for (int s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 679 | for (int s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1146 | for (int s=0; s::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1211 | for (int s=0; s >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function ‘void Plink::readGenericVariantData()’: gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 125 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 192 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 247 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 298 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 381 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 395 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 403 | for (int i=0; isecond; | ^~ gvar.cpp:414:8: warning: unused variable ‘fatal’ [-Wunused-variable] 414 | bool fatal = false; | ^~~~~ gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 549 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 553 | for (int l=0; l::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 556 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function ‘void Plink::readCNVList()’: cnv.cpp:247:8: warning: unused variable ‘p1’ [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:247:11: warning: unused variable ‘p2’ [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:332:12: warning: unused variable ‘p1’ [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:332:15: warning: unused variable ‘p2’ [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:678:36: warning: variable ‘is’ set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 815 | for (int s1=0; s1::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 825 | for (int s2=s1+1; s2::iterator i2 = isection.begin(); | ^~ cnv.cpp:1103:36: warning: variable ‘il’ set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ 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; | ^~~~ 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; | ^~~ cnv.cpp: In member function ‘void Plink::positionPermuteSegments()’: cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2013 | for (int c = 0 ; c < scaffold.size(); c++) | ~~^~~~~~~~~~~~~~~~~ cnv.cpp: In member function ‘vector_t Plink::glmCNVBurdenModel(Perm&, bool)’: cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] 2098 | noCovar == true; | ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 2202 | indivPair p = ic->first; | ^ cnv.cpp:2288:10: warning: unused variable ‘statistic’ [-Wunused-variable] 2288 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable ‘pvalue’ [-Wunused-variable] 2289 | double pvalue = pval[ pval.size()-1 ]; | ^~~~~~ cnv.cpp:2290:10: warning: unused variable ‘beta’ [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 step.cpp:18: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from greport.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ greport.cpp: In member function ‘void Plink::displayGeneReport()’: greport.cpp:78:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 78 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 147 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:19: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 148 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 156 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 169 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 240 | for (int l=0; l< ari->second.size(); l+=2) | ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable ‘cnt’ [-Wunused-variable] 125 | int cnt = 0; | ^~~ In file included from helper.h:24, from flip.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ qualscores.cpp: In member function ‘void Plink::filterQualGenotypes()’: qualscores.cpp:122:12: warning: unused variable ‘nfound’ [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from cfamily.cpp:18: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function ‘int mCount(Individual*, Individual*)’: cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:221:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp: In function ‘bool isAncestorOf(Individual*, Individual*)’: cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 263 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -fdebug-prefix-map=/build/plink-MddXAD/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 setscreen.cpp:21: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function ‘void Plink::setAssocSummary()’: setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 80 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 110 | if ( tokens.size() != cols ) | ~~~~~~~~~~~~~~^~~~~~~ setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ In file included from idhelp.cpp:18: idhelp.h: In member function ‘void IDGroup::display()’: idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 196 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘std::map > IDHelper::parseQuery(std::string)’: idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:63:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 63 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘bool IDHelper::matchIndividual(IDGroup*, std::map >&)’: idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 169 | if ( found != matchTemplate.size() ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable ‘match’ [-Wunused-variable] 128 | bool match = true; | ^~~~~ idhelp.cpp: In member function ‘void IDHelper::setJointValues(IDGroup*)’: idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 296 | for ( int i = 0 ; i < mask.size() ; i++) | ~~^~~~~~~~~~~~~ idhelp.cpp:214:26: warning: unused variable ‘jo’ [-Wunused-variable] 214 | vector & jo = jointOrder[j]; | ^~ idhelp.cpp: In member function ‘std::set IDHelper::findAllIndividuals(std::map >&)’: idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘void IDHelper::idHelp()’: idhelp.cpp:502:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 502 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 510 | if ( p < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 542 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:547:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 547 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:529:10: warning: unused variable ‘seenJoint’ [-Wunused-variable] 529 | bool seenJoint = true; | ^~~~~~~~~ idhelp.cpp:584:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 584 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:594:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 594 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:678:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 678 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 727 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 742 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 745 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:747:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 747 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 757 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable ‘jf’ [-Wunused-variable] 744 | set & jf = jointField[j]; | ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 772 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 790 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 794 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:31: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 894 | int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 903 | if ( j < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 922 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 950 | for ( int i=0; i::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 975 | if ( v->value.size() + 3 > myField->width ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1000 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1003 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1013 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1015:17: warning: unused variable ‘group’ [-Wunused-variable] 1015 | IDGroup * group = idgroup[g]; | ^~~~~ idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1025 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1028 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:14: warning: unused variable ‘v’ [-Wunused-variable] 1031 | IDValue & v = *(group->values[j]); | ^ idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1070 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1128 | for ( int k = 0; k < (*i0)->values.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1183 | for (int z=0; zvalues.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1189 | for (int z=0; z<(*i0)->values.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1236 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1242 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:14: warning: unused variable ‘v’ [-Wunused-variable] 1245 | IDValue & v = *(group->values[j]); | ^ idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1346 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1424 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1440 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘void IDHelper::idReplace()’: idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1551 | for ( int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1631 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1648 | for (int f = 0 ; f < targetFields.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1649 | for (int i = 0 ; i < tokens.size(); i++) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1654 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1675 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1684 | if ( tokens.size() <= maxfield ) | ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1692 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1710 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1733 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1735 | for (int i = 0 ; i < thisGroup->values.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1770 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1784 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘void IDHelper::idMatch()’: idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1903 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1937 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1957 | for (int f = 0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1964 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1986 | for (int f = 0 ; f < fieldNames.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 2018 | if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2024 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2030 | if ( maxF >= tok.size() ) | ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2034 | for (int f=0; f::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable ‘jointQuery’ [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2167 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2168 | for (int j=0; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2201 | for (int k = 0 ; k < thisLine.size() ; k++ ) | ~~^~~~~~~~~~~~~~~~~ idhelp.cpp: In member function ‘void IDHelper::idDump()’: idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2229 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 cnv.cpp: In member function ‘void Plink::processCNVList()’: cnv.cpp:1500:13: warning: ‘cdet.CInfo::lstart’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1500 | CInfo cdet; | ^~~~ cnv.cpp:1500:13: warning: ‘cdet.CInfo::lstop’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function ‘void Plink::lookup2()’: lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 203 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 280 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 In file included from blox.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i > Plink::mkBlks(int, int)’: blox.cpp:147:11: warning: unused variable ‘nsnps’ [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; | ^~~~~ blox.cpp:156:11: warning: unused variable ‘numStrong’ [-Wunused-variable] 156 | int numStrong = 0; | ^~~~~~~~~ blox.cpp:157:11: warning: unused variable ‘numRec’ [-Wunused-variable] 157 | int numRec = 0; | ^~~~~~ blox.cpp:158:11: warning: unused variable ‘numInGroup’ [-Wunused-variable] 158 | int numInGroup = 0; | ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable ‘cnt’ [-Wunused-variable] 226 | int cnt = 0; | ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 418 | for (int k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 427 | for (int k=0; k >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 blox.cpp:569:41: warning: ‘pB2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 569 | if ( pB1>0 ) loglike1 += knownBA * log( pB1 ); | ~~~^~~~~~~ blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 505 | double p1 = pA1 + pB1; | ^~ blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 503 | double pA = pA1 + pA2; | ^~ blox.cpp:510:10: warning: ‘pA1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 510 | double D = pA1 - (pA*p1); | ^ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 dosage.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function ‘void HaploPhase::reset()’: phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 513 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 548 | for (int f = 0 ; f < vzin.size() ; f++ ) | ~~^~~~~~~~~~~~~ dosage.cpp:581:20: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 581 | if ( tok.size() < firstCol ) | ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 601 | for (int i=firstCol; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 695 | for (int i = 0; i < personMap[f].size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:24: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) dosage.cpp:989:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 989 | for (int q=0; qgetStatistic() : 0; | ^~~~~~~~~ dosage.cpp:1252:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1252 | if ( o->second != dosageFilename_all.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1310 | if ( ++qq == qthresh.size() ) | ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable ‘geno_field’ [-Wunused-variable] 190 | int geno_field = a2_field + skip2 + 1; | ^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 annot.cpp:20: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function ‘void Plink::annotateFile()’: annot.cpp:83:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 83 | for (int j=1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 149 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 250 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 251 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 260 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:23: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 275 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:9: warning: unused variable ‘include’ [-Wunused-variable] 300 | bool include = false; | ^~~~~~~ In file included from metaanal.cpp:21: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor ‘Alleles::Alleles(std::string, int, int, std::string, std::string)’: metaanal.cpp:47:7: warning: ‘Alleles::bp’ will be initialized after [-Wreorder] 47 | int bp; | ^~ metaanal.cpp:44:10: warning: ‘std::string Alleles::a1’ [-Wreorder] 44 | string a1; | ^~ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] 61 | Alleles(string name, int chr, int bp, string a1, string a2) | ^~~~~~~ metaanal.cpp: In member function ‘void Plink::metaAnalysis()’: metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 159 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 182 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 213 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | for (int i=0; i >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ metaanal.cpp:253:11: warning: variable ‘pval_column’ set but not used [-Wunused-but-set-variable] 253 | int pval_column = -1; | ^~~~~~~~~~~ metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 482 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 637 | for (int f=0; f >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 680 | for (int f=0; fone[personPosition[f][i]] = s1; | ^ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 helper.h:24, from r.cpp:19: options.h: In member function ‘void OptionSet::display()’: options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29: Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’: Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 203 | { name=""; fix_content(); } | ^~ Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’: Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 206 | { name=""; fix_content(); } | ^~ Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’: Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } | ~^~~~~ Rconnection.h: In member function ‘void Rstrings::decode()’: Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare] 245 | while (i < len) { if (!c[i]) nel++; i++; } | ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ r.cpp: In member function ‘void Plink::Rfunc()’: r.cpp:330:8: warning: unused variable ‘ct’ [-Wunused-variable] 330 | int ct = data->length(); | ^~ r.cpp:380:9: warning: ‘rCov’ may be used uninitialized in this function [-Wmaybe-uninitialized] 380 | delete rCov; | ^~~~ r.cpp:378:14: warning: ‘rS’ may be used uninitialized in this function [-Wmaybe-uninitialized] 378 | delete rS; | ^~ r.cpp:377:14: warning: ‘rP’ may be used uninitialized in this function [-Wmaybe-uninitialized] 377 | delete rP; | ^~ r.cpp:376:14: warning: ‘rN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 376 | delete rN; | ^~ r.cpp:399:10: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 399 | delete rc; | ^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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:249:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ | ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor ‘virtual Rconnection::~Rconnection()’: Rconnection.cpp:567:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 567 | if (host) free(host); host=0; | ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 567 | if (host) free(host); host=0; | ^~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 g++ -Wall -g -fdebug-prefix-map=/build/plink-MddXAD/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 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' make[1]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/build/plink-MddXAD/plink-1.07+dfsg' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-3_amd64.deb'. dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../plink_1.07+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/plink-MddXAD /tmp/plink-1.07+dfsg-3o41dk543 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.2hF6CA6ubR... I: success in 1470.7078 seconds md5: plink-dbgsym_1.07+dfsg-3_amd64.deb: OK md5: plink_1.07+dfsg-3_amd64.deb: OK sha1: plink-dbgsym_1.07+dfsg-3_amd64.deb: OK sha1: plink_1.07+dfsg-3_amd64.deb: OK sha256: plink-dbgsym_1.07+dfsg-3_amd64.deb: OK sha256: plink_1.07+dfsg-3_amd64.deb: OK Checksums: OK