W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 19 18:07:20 +14 2023 I: pbuilder-time-stamp: 1681877240 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [plink_1.07+dfsg-4.dsc] I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 1 05:36:45 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting plink in plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-4.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 dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7946/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 19 18:07 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/7946/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/7946/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=7946 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fhjn5Dw2/pbuilderrc_7wiZ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fhjn5Dw2/b2 --logfile b2/build.log --extrapackages usrmerge plink_1.07+dfsg-4.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 10:21 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:21 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 19 18:07 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/7946/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After unpacking 74.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Fetched 19.9 MB in 0s (52.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/7946/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/7946/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_clean make -j7 clean make[2]: Entering directory '/build/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make -j7 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from tinput.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from binput.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 271 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 309 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 591 | if ( c > sample.size()) | ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 603 | if ( gn != 2 * sample.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 157 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 176 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 186 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 261 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] 339 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] 351 | while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ In file included from plink.cpp:28: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 516 | if ( i == include.size() ) | ~~^~~~~~~~~~~~~~~~~ input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 521 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ input.cpp:545:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 545 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 579 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 631 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readSet()': input.cpp:695:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 695 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 787 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 821 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] 897 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 927 | for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 961 | else if ( ccount != tokens.size() ) | ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1043 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1064 | for (int i=0; ifreq * ( 1 - locus[l]->freq ); | ^~ input.cpp: In member function 'void Plink::makePhenotype()': input.cpp:1208:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1208 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1232 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1256 | if (tokens.size() < 2+par::mult_covar) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1261 | for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] 1335 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1227 | for (int i=0;i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from plink.cpp:35: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1519 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 1538 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 1572 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1599 | else if (tokens.size() != par::plist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1602 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 1764 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 1792 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 196 | for (int k=0; k&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2116 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2172 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2200 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2210 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2225 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 58 | for (int i=0; i >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 76 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 79 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2397 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 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 'unsigned int'} [-Wsign-compare] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ input.cpp:2453:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2453 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2471 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 193 | for (int t=0; t > CArgs::value(std::string, int)': helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) | ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 307 | if (s[i] == ',' || i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ helper.cpp:309:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 323 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 461 | for (int i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 659 | for (int i=0;i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 729 | for (int h=0; h::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] 959 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 966 | for (int i=0;i::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 1040 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2106 | for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'unsigned int'} 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 '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 '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:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1389 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1391 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2359 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2362 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 2366 | for (int l=0; l&)': 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 'unsigned int'} [-Wsign-compare] 2455 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2462 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2491 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2510 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2530 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2549 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2568 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2587 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2606 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2671 | for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2722 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2756 | for (int j=1; j, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2935 | for (int i=0; i&)': helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp 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; | ^~~~~~~~~~~~~~ In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] 458 | int m,l,iter,i,k; | ^ stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] 813 | const double eps = 1e-12; | ^~~ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] 818 | int r = u.size(); | ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] 906 | const double eps = 1e-12; | ^~~ 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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1477 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1483 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1515 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1521 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1531 | for (int i = 0; i < v.size(); i++) | ~~^~~~~~~~~~ helper.cpp: In function 'int getInt(std::string, std::string)': helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'double getDouble(std::string, std::string)': helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 95 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 123 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 132 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 155 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 163 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 198 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 273 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 591 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 739 | for ( int l = 0 ; l < locus.size() ; l++ ) | ~~^~~~~~~~~~~~~~ filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 762 | for ( int i = 0 ; i < sample.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1078 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 1091 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 1143 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 1165 | for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 295 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 304 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 357 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 372 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 452 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 511 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 651 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 784 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 786 | for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] 919 | for (int k=0;k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 954 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 955 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 975 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 976 | for (int j=i+1; j::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ cluster.cpp:1049:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1049 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1050 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1060 | for (int j1=0; j1 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1061 | for (int j2=0; j2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1107 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1163 | for (int j=0; j::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1203 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1228 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1254 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1272 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1290 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1661 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] 191 | for (int i2=0; i2::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 279 | if ( elist.size() != par::cluster_mds_dim ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] 242 | bool flag = svd(D,eigenvalue,eigenvector); | ^~~~ In file included from output.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 86 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 89 | for (int k=0; k::iterator loc1 = locus.begin()+m1; | ^~~~ output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] 403 | vector::iterator loc2 = locus.begin()+m2; | ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 520 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 526 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 553 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2200 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2322 | for (int j=0; j >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 2380 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2409 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 102 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 105 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 395 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 741 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 785 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 788 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) | ~~~~^~~~~ input.cpp:60:10: note: 'PED' was declared here 60 | FILE * PED; | ^~~ In file included from prephap.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::display_indivReport()': output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] 69 | << setw(6) << genotype(*this,i1,l) << "\n"; | ~~~~~~~~^~~~~~~~~~~~ output.cpp:46:7: note: 'i1' was declared here 46 | int i1; | ^~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 146 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] 154 | for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] 161 | for (int e=0;e >::size_type' {aka 'unsigned int'} [-Wsign-compare] 226 | if (len != tokens.size() - offset ) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] 701 | int c=0; | ^ prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 283 | for ( int i = allele ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 412 | while ( index < tokens.size() ) | ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 416 | if ( tokens[index].size() != len ) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 470 | for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 560 | for (int i=0; i::difference_type)' at /usr/include/c++/12/bits/stl_bvector.h:328:14, inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/12/bits/stl_bvector.h:350:16, inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/12/bits/stl_bvector.h:343:24, inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_bvector.h:1036:23, inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: /usr/include/c++/12/bits/stl_bvector.h:200:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] 200 | __n = __n % int(_S_word_bit); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1405:11: note: 'maxI' was declared here 1405 | int maxI; | ^~~~ assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1109:68: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] 1109 | pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); | ~~~~~^~~~~~~~~~ assoc.cpp:1019:14: note: 'pvalue' was declared here 1019 | double pvalue; | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp In file included from /usr/include/c++/12/iostream:39, from assoc.cpp:14: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: /usr/include/c++/12/ostream:221:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:36: note: 'gen_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: /usr/include/c++/12/ostream:221:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:25: note: 'rec_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: /usr/include/c++/12/ostream:221:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:14: note: 'dom_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: /usr/include/c++/12/ostream:221:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1385:22: note: 'mult_chisq' was declared here 1385 | double mult_p, mult_chisq; | ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from phase.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 373 | for (int i=0; i&)': phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 472 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] 678 | for (int z=0; z, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1238 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 1280 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 1299 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) | ~~^~~~~~~~~~~~~~ In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1829 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1843 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 91 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 258 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 272 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:335:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 335 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 342 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 350 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 469 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 474 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 492 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 504 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 871 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 882 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 895 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 936 | for (int f=0;f::size_type' {aka 'unsigned int'} [-Wsign-compare] 943 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:13: warning: unused variable 'tmp' [-Wunused-variable] 962 | int tmp = deleteIndividuals(indel); | ^~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1038 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 1048 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 1236 | for ( int k=0; kpm->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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:81:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 81 | for (int i=0; iperson.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:30: warning: unused variable 'person' [-Wunused-variable] 96 | Individual * person = klist[k]->person[i]; | ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 132 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 144 | for (int c=0; c < fam->kid.size(); c++) | ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 234 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 327 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 412 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 522 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 557 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 668 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 334 | for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 489 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 497 | for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1025 | for (int l=0; l::size_type' {aka '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; | ^~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 37 | for(int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 52 | for(int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 59 | else if (par::set_min > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:48: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 99 | for(int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 129 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 176 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 216 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ In file included from perm.h:17, from perm.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 236 | for (int i=0;i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 317 | for (int i=0;i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 329 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 367 | for (int i=0;i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 412 | for (int i=0;i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 618 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 619 | for (int j=0;j > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 631 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 632 | for (int j=0;j > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 642 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 643 | for (int j=0;j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 703 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 713 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 905 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 975 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 144 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 145 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 187 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 199 | for(int i=0; i&, std::vector&)': perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1249 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 64 | for (int i=0; i&, 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 'unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:805:103: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] 805 | gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; | ^ genepi.cpp:614:17: note: 'cancor1_pos' was declared here 614 | int cancor1_pos; | ^~~~~~~~~~~ In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 333 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 377 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 395 | for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] 403 | for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] 426 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 722 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 784 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 830 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 842 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 173 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 85 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)': haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 48 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 62 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:79:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 79 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:41: 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:340:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 357 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:375:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 375 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ In file included from haploTDT.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 93 | for (int f=0; f > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 195 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 293 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 328 | for (int c=0; c, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] 1103 | if (write) | ^~ merge.cpp:943:8: note: 'write' was declared here 943 | bool write; | ^~~~~ g++ -Wall -g -ffile-prefix-map=/build/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 bmerge.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp In file included from helper.h:24, from webcheck.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 117 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 130 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 146 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 218 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 357 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 390 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 409 | for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] 417 | for (int l=0;l::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 697 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] 839 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 871 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 883 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 89 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 267 | for (int i=0; i < family.size(); i++) | ~~^~~~~~~~~~~~~~~ In file included from parse.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 315 | for (int f = 0 ; f < family.size() ; f++) | ~~^~~~~~~~~~~~~~~ In file included from helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 648 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 657 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 50 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 368 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 377 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 381 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 384 | for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] 390 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 395 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 415 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 424 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 460 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 461 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 462 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 467 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | for (int i=0; ibp - locus[last]->bp ) / 1000.0 | ^ legacy.cpp:35:7: note: 'last' was declared here 35 | int last; | ^~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) | ^~ segment.cpp:875:11: 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:954:22: warning: unused variable 'p1' [-Wunused-variable] 954 | Individual * p1 = sample[i1]; | ^~ segment.cpp:955:22: warning: unused variable 'p2' [-Wunused-variable] 955 | Individual * p2 = sample[i2]; | ^~ segment.cpp:1027:26: warning: unused variable 'p1' [-Wunused-variable] 1027 | Individual * p1 = sample[i1]; | ^~ segment.cpp:1028:26: 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 'unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 773 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 861 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] 1855 | indivPair p = ic->first; | ^ 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 'unsigned int'} and 'int' [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1331 | for (int i=0; i< (*pA)->segs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1437 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1441 | if ( (*pA)->match[i].size() >= maxlist ) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1461 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ 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:2378:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2378 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2380:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2380 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2382:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2382 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2412:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2412 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2414:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2414 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2416:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2416 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2443:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2443 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2445:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2445 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2447:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2447 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2474:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2474 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2476:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2476 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; In file included from model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp In file included from model.cpp:17: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&)': model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 132 | if ( include.size() != P->n ) | ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 354 | for (int i=0; i< par::parameter_list.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 367 | for ( int i = 0 ; i < X.size() ; i++) | ~~^~~~~~~~~~ model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] 849 | error("Internal problem with QFAM model specification"); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-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 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 294 | for (int h=1; h < whap->current->group.size(); h++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 344 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 355 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 423 | for (int c=0; c *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; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] 610 | double pvalue = chiprobP(chisq,df); | ~~~~~~~~^~~~~~~~~~ glm.cpp:556:15: note: 'df' was declared here 556 | int df; | ^~ g++ -Wall -g -ffile-prefix-map=/build/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 helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 493 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 609 | for (int l=0; l< original.size(); l++) | ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] 654 | const double pthresh = 0.01; | ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] 655 | bool one_sided = true; | ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] 707 | int srange_cnt = 0; | ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] 708 | bool inRange = false; | ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 895 | for (int i = 0 ; i < tokens.size() ; i++) | ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 76 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 86 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 96 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 106 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 157 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 271 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 378 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] 218 | bool informative = false; | ^~~~~~~~~~~ dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 504 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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:267:21: 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:501:25: 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:1554:23: 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 -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] 374 | double wt; | ^~ In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 206 | for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 272 | for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 289 | for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 128 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 136 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 146 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 164 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 200 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 209 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1142:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] 1142 | ++(*p_gcnt); | ~^~~~~~~~ elf.cpp:1112:13: note: 'p_gcnt' was declared here 1112 | int * p_gcnt; | ^~~~~~ elf.cpp:1147:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1147 | ++(*p_cnt); | ~^~~~~~~ elf.cpp:1111:13: note: 'p_cnt' was declared here 1111 | int * p_cnt; | ^~~~~ In file included from pdriver.cpp:18: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 314 | for (int i=1; i::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1401 | for (int c1 = 0; c1 < collection.size() ; c1++ ) | ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:19: warning: unused variable 't1' [-Wunused-variable] 1448 | int t1=0; | ^~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ In file included from haploQTL.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)': haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 297 | for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] 337 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] 396 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 413 | for (int z2=0; z2::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 655 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 754 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 802 | for (int z=0; z::size_type' {aka '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 '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 '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 'unsigned int'} and 'int' [-Wsign-compare] 851 | ||alleles2.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1225 | for (int z = 0; z < hap1[p1].size(); z++) | ~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) | ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++) | ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] 1250 | int j=0; | ^ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1419 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1477 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 183 | while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 683 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 691 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 751 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 791 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 798 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 868 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 872 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 949 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka '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; | ^~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:65, from options.h:18: In member function 'void std::_Bit_iterator_base::_M_incr(std::ptrdiff_t)', inlined from 'std::_Bit_iterator::iterator& std::_Bit_iterator::operator+=(std::iterator::difference_type)' at /usr/include/c++/12/bits/stl_bvector.h:328:14, inlined from 'std::_Bit_iterator::iterator std::operator+(const _Bit_iterator::iterator&, iterator::difference_type)' at /usr/include/c++/12/bits/stl_bvector.h:350:16, inlined from 'std::_Bit_iterator::reference std::_Bit_iterator::operator[](std::iterator::difference_type) const' at /usr/include/c++/12/bits/stl_bvector.h:343:24, inlined from 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_bvector.h:1036:23, inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:1191:9: /usr/include/c++/12/bits/stl_bvector.h:200:11: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] 200 | __n = __n % int(_S_word_bit); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:422:7: note: 'ref' was declared here 422 | int ref; | ^~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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 'unsigned int'} [-Wsign-compare] 92 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 128 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 137 | for ( int f=0; f >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 173 | if ( tokens.size() <= snp_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 201 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) | ~~^~~~~~~~~~~ clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 480 | if( l1 < P->locus.size()-1 ) | ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 157 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 189 | for( int a = 0; a < posshap1.size(); a++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 190 | for( int b = 0; b < posshap2.size(); b++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 225 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 315 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 328 | for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] 347 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 358 | for (int z2=0; z2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 89 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 97 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 106 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 128 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 132 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 162 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 166 | for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 105 | for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 107 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 124 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 151 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 160 | for (int i=0; i > NList::tokenize(std::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] 189 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 239 | if ( s[i]== range_char && i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ In file included from profile.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 390 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 402 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] 480 | bool a1 = i2->second; | ^~ profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] 525 | bool sawNamedAllele = false; | ^~~~~~~~~~~~~~ profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 667 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 393 | for (int g=0; g::size_type' {aka 'unsigned int'} [-Wsign-compare] 454 | for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] 456 | for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'unsigned int'} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 962 | for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] 986 | for (int i=0; i >::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] 1129 | for (int i=0; i< lst.size(); i++) | ~^~~~~~~~~~~~ whap.cpp:1142:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1142 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1162 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1197 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1231 | for (int i=0; i >::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] 1389 | for (int l=0;l >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1425 | for (int h=0; h < m.group.size(); h++) | ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] 172 | double gh_11_12 = h11*h12; | ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 635 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 679 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 1146 | for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] 1211 | for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 125 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 192 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 247 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 298 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 381 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 395 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 549 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 553 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 556 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:247:18: warning: unused variable 'p2' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:332:19: warning: unused variable 'p1' [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp cnv.cpp:678:43: 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 'unsigned int'} [-Wsign-compare] 815 | for (int s1=0; s1::size_type' {aka 'unsigned int'} [-Wsign-compare] 825 | for (int s2=s1+1; s2::iterator i2 = isection.begin(); | ^~ cnv.cpp:1103:43: 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 '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 ]; | ^~~~ In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 78 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 147 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 148 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 156 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 169 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/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 qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 80 | for (int i=0; i >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp 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 'unsigned int'} [-Wsign-compare] 196 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: 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 'unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 63 | for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 '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 '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 'unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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]; | ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp idhelp.cpp: 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 'unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 510 | if ( p < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 542 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 547 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:529:24: warning: unused variable 'seenJoint' [-Wunused-variable] 529 | bool seenJoint = true; | ^~~~~~~~~ idhelp.cpp:584:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 584 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:594:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 594 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 678 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 727 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 745 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:747:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 747 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:38: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 894 | int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 903 | if ( j < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 922 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 950 | for ( int i=0; i::size_type' {aka 'unsigned int'} 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 '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 1028 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:21: 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 'unsigned int'} [-Wsign-compare] 1070 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1128 | for ( int k = 0; k < (*i0)->values.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1183 | for (int z=0; zvalues.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 1242 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:21: 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 'unsigned int'} [-Wsign-compare] 1346 | for (int i=0; i::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1440 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 1551 | for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1631 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1648 | for (int f = 0 ; f < targetFields.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1654 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1675 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1684 | if ( tokens.size() <= maxfield ) | ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1692 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1710 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1733 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 1735 | for (int i = 0 ; i < thisGroup->values.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1770 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1784 | for (int f=0; f >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1903 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1937 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1957 | for (int f = 0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1964 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1986 | for (int f = 0 ; f < fieldNames.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:29: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 2018 | if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2024 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2030 | if ( maxF >= tok.size() ) | ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2034 | for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2167 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 2168 | for (int j=0; j >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 2229 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 '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 'unsigned int'} [-Wsign-compare] 418 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 427 | for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ blox.cpp:569:41: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] 569 | if ( pB1>0 ) loglike1 += knownBA * log( pB1 ); | ~~~^~~~~~~ blox.cpp:489:22: note: 'pB2' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:505:10: warning: 'pB1' may be used uninitialized [-Wmaybe-uninitialized] 505 | double p1 = pA1 + pB1; | ^~ blox.cpp:489:18: note: 'pB1' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:503:10: warning: 'pA2' may be used uninitialized [-Wmaybe-uninitialized] 503 | double pA = pA1 + pA2; | ^~ blox.cpp:489:14: note: 'pA2' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:510:10: warning: 'pA1' may be used uninitialized [-Wmaybe-uninitialized] 510 | double D = pA1 - (pA*p1); | ^ blox.cpp:489:10: note: 'pA1' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 513 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 548 | for (int f = 0 ; f < vzin.size() ; f++ ) | ~~^~~~~~~~~~~~~ dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 581 | if ( tok.size() < firstCol ) | ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 601 | for (int i=firstCol; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 695 | for (int i = 0; i < personMap[f].size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 989 | for (int q=0; qgetStatistic() : 0; | ^~~~~~~~~ dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1252 | if ( o->second != dosageFilename_all.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka '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; | ^~~~~~~~~~ In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 83 | for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 149 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 250 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 251 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 260 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 275 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] 300 | bool include = false; | ^~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp 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 'unsigned int'} [-Wsign-compare] 159 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 182 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 213 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 261 | for (int i=0; i >::size_type' {aka '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 'unsigned int'} [-Wsign-compare] 482 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 637 | for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] 680 | for (int f=0; f=nel)?0:cont[i]; } | ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] 245 | while (i < len) { if (!c[i]) nel++; i++; } | ~~^~~~~ Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ | ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 567 | if (host) free(host); host=0; | ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 567 | if (host) free(host); host=0; | ^~~~ In file included from helper.h:24, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp r.cpp:380:16: warning: 'rCov' may be used uninitialized [-Wmaybe-uninitialized] 380 | delete rCov; | ^~~~ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ r.cpp:378:14: warning: 'rS' may be used uninitialized [-Wmaybe-uninitialized] 378 | delete rS; | ^~ r.cpp:164:14: note: 'rS' was declared here 164 | Rinteger * rS; | ^~ r.cpp:377:14: warning: 'rP' may be used uninitialized [-Wmaybe-uninitialized] 377 | delete rP; | ^~ r.cpp:163:13: note: 'rP' was declared here 163 | Rdouble * rP; | ^~ r.cpp:376:14: warning: 'rN' may be used uninitialized [-Wmaybe-uninitialized] 376 | delete rN; | ^~ r.cpp:162:14: note: 'rN' was declared here 162 | Rinteger * rN; | ^~ r.cpp:399:10: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 399 | delete rc; | ^~ r.cpp:68:16: note: 'rc' was declared here 68 | Rconnection *rc; | ^~ dosage.cpp:915:35: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] 915 | SNP[snp_code]->one[personPosition[f][i]] = s1; | ^ dosage.cpp:725:15: note: 'snp_code' was declared here 725 | int snp_code; | ^~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with '-fvar-tracking-assignments', retrying without 80 | void setOptions(CArgs & a) | ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -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-1.07+dfsg' make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/plink/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_i386.deb'. dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../plink_1.07+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../plink_1.07+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/7946/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/7946/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7946 and its subdirectories I: Current time: Wed Apr 19 18:11:58 +14 2023 I: pbuilder-time-stamp: 1681877518