I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 14 05:34:44 +14 2021 I: pbuilder-time-stamp: 1634139284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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: Copying source file I: copying [plink_1.07+dfsg-2.dsc] I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 19 20:15:45 2018 +14 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "bob.dybian@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plink_1.07+dfsg-2.dsc 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-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2710/tmp/hooks/D01_modify_environment starting debug: Running on codethink-sled15-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/2710/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2710/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2710 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/tmp.vRWa7CgERK/pbuilderrc_e1u3 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.vRWa7CgERK/b2 --logfile b2/build.log plink_1.07+dfsg-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-189-generic #219-Ubuntu SMP Tue Aug 11 12:24:40 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Oct 14 05:34 sh -> bash lrwxrwxrwx 1 root root 4 Oct 4 04:48 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/2710/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: arm64 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 (>= 11), 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 ... 19168 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 (>= 11); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After unpacking 69.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 18.8 MB in 7s (2665 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../27-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../33-zlib1g-dev_1%3a1.2.11.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... 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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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_clean make -j8 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-1.07+dfsg' /usr/bin/make 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 In file included from plink.cpp:28: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from plink.cpp:35: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 input.cpp In file included from input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i == include.size() ) ~~^~~~~~~~~~~~~~~~~ input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_clst) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:821:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if ( ccount != tokens.size() ) ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_pheno) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_covar) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1261:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::clist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1519:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::plist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::__cxx11::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ 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 In file included from tinput.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( c > sample.size()) ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * sample.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 genome.cpp In file included from genome.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^~~~~~~ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^~~~~~ genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^~ genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^~~ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^~~ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^~~ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~^~~~~~~~ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::__cxx11::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int t=0; t > CArgs::value(std::__cxx11::string, int)': helper.cpp:267:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (i+j) < a.size() ) ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (r.size() != c) error("Not enough arguments given for option: "+s+" "); ~~~~~~~~~^~~~ helper.cpp: In function 'std::vector > parse2str(std::__cxx11::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0 ; i < s.length() ; i++) ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (s[i] == ',' || i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ helper.cpp:309:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (i == s.length()-1) t += s[i]; ~~^~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector parse2int(std::__cxx11::string)': helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] while(h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s = 0 ; s < snps.size() ; s++) ~~^~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string chromosomeName(int)': helper.cpp:952:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( c < 0 || c >= par::chr_code.size() ) ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'int getMarkerChromosome(Plink&, std::__cxx11::string)': helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i getChromosomeRange(Plink&)': helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->fid.length() > par::pp_maxfid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->iid.length() > par::pp_maxiid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (locus[l]->name.length() > par::pp_maxsnp) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( input.size() != P.nl_all ) ~~~~~~~~~~~~~^~~~~~~~~~~ helper.cpp: In function 'std::map, std::set > readRange(std::__cxx11::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^~~~ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^~~~~~~~~~~~~~ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^~~~~~~~~~~~~~ helper.cpp: In member function 'std::__cxx11::string CArgs::value(std::__cxx11::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'int CArgs::value_int(std::__cxx11::string)': helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::__cxx11::string)': helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'double CArgs::value_double(std::__cxx11::string)': helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'int getInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:378:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:391:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'double getDouble(std::__cxx11::string, std::__cxx11::string)': helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid numeric argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wmaybe-uninitialized] cur[maxI] = false; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3342:12: warning: 'ci.CInfo::lstop' may be used uninitialized in this function [-Wmaybe-uninitialized] CInfo ci; ^~ helper.cpp:3342:12: warning: 'ci.CInfo::bpstop' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] const double eps = 1e-12; ^~~ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^~~ stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < v.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 filters.cpp In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int l = 0 ; l < locus.size() ; l++ ) ~~^~~~~~~~~~~~~~ filters.cpp:762:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < sample.size() ; i++ ) ~~^~~~~~~~~~~~~~~ filters.cpp:1078:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 multi.cpp In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=1; z<=qt.size(); z++) ~^~~~~~~~~~~ cluster.cpp:452:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0;k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=i+1; j::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cluster.cpp:1038:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int j=0;j >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; ~~~~~~~~~^~~~~ cluster.cpp:1049:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j1=0; j1 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j2=0; j2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i2=0; i2::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( elist.size() != par::cluster_mds_dim ) ~~~~~~~~~~~~~^~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp In file included from output.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] vector::iterator loc2 = locus.begin()+m2; ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < setname.size();i++) ~~^~~~~~~~~~~~~~~~ output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] int best = 0 ; ^~~~ 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:1108:4: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( pvalue <= par::set_score_p && pvalue >= 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 epi.cpp In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (len != tokens.size() - offset ) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ prephap.cpp:283:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = allele ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ prephap.cpp:412:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] while ( index < tokens.size() ) ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:34: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens[index].size() != len ) ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( index == tokens.size() - 1 ) ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( nh != hapmap.size() ) ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < pp[i].size() ; z++ ) ~~^~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < h1.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 trio.cpp In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:272:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:335:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp:350:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0;f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kpm->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kpp->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iperson.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c < fam->kid.size(); c++) ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] } ^ 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] } ^ genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] bool casewise_deletion = false; ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if (par::set_min > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (par::set_max==-1 || par::set_max > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=j+1; k < snpset[i].size(); k++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i&, std::vector&)': perm.cpp:273:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] if (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 hotel.cpp In file included from hotel.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] if (!sample[i]->missing) ^ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::__cxx11::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); ^ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ 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 haploTDT.cpp In file included from haploTDT.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size() - 1) ~~^~~~~~~~~~~~~~~~~~~ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < family.size(); i++) ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < family.size() ; f++) ~~^~~~~~~~~~~~~~~ qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < (*f)->kid.size() ; k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] long int inc; ^~~ bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~~~ bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without 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 -c mishap.cpp In file included from mishap.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:861:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1178:31: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< (*pA)->segs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:33: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( (*pA)->match[i].size() >= maxlist ) ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] homozygWindows[l] == 0; g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::__cxx11::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!ibd) ^~ segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' SIBS << setw(10) << original[l] << " " ^~~~ segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ifirst; ^ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] int nseg = smap.size(); ^~~~ segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ 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 model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from model.cpp:17: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( include.size() != P->n ) ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< par::parameter_list.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < X.size() ; i++) ~~^~~~~~~~~~ model.cpp:374:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] double maxVIF = 0; ^~~~~~ model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] error("Internal problem with QFAM model specification"); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from glm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=1; h < whap->current->group.size(); h++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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:6025:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~~~~~^~~~~~~~~~~~~ dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; ^~~ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~~~~~~~~~~~^~~~~~~~~~~~~~ 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 elf.cpp In file included from helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] const double pthresh = 0.01; ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] bool one_sided = true; ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] int srange_cnt = 0; ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] bool inRange = false; ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++) ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != ncol ) ~~~~~~~~~~~~~~^~~~~~~ elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:374:10: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] double wt; ^~ elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1154:8: warning: 'p_gcnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_gcnt); ^~~~~~~~~~~ elf.cpp:1165:5: warning: 'p_cnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_cnt); ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:106:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] bool informative = false; ^~~~~~~~~~~ dfam.cpp:504:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] int totalInformative = 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 fisher.cpp In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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:261:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "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:448:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:449:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (*ncol <= 1) ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' for (i = 1; i <= *ldkey << 1; ++i) { ^~~ fisher.cpp:501:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "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:1539:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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 In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:164:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::__cxx11::string, int, std::__cxx11::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] char out_buf[BUF_SIZE+1]; // Output buffer for GET request ^~~~~~~ sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] char in_buf[BUF_SIZE+1]; // Input buffer for response ^~~~~~ sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] unsigned int i; // Loop counter ^ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] int echoStringLen = 100; ^~~~~~~~~~~~~ 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 In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( added.size() >= par::proxy_snp_filter ) ~~~~~~~~~~~~~^~~~~~ proxy.cpp:854:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c1 = 0; c1 < collection.size() ; c1++ ) ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] int t1=0; ^~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] CSNP * s = SNP[l]; ^ 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 pdriver.cpp In file included from pdriver.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploQTL.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 haplohelper.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l < actual_map.size(); l++) ~~^~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] ||alleles2.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[p1].size(); z++) ~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z1 = 0; z1 < hap1[p1].size(); z1++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2 = 0; z2 < hap1[p2].size(); z2++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] int j=0; ^ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 haplowindow.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < pp[i].size(); z++) ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] int pcnt=1; ^~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 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 clumpld.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:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i clump_LD::read_assoc_file(std::__cxx11::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f=0; f >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < sp.size(); i++) ~~^~~~~~~~~~~ clumpld.cpp:480:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( l1 < P->locus.size()-1 ) ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( j < grouped_snps.size()-1) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int a = 0; a < posshap1.size(); a++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int b = 0; b < posshap2.size(); b++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->hap1[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->pp[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s < g.size(); 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 metaem.cpp In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] bool OLD_clist = par::clist; ^~~~~~~~~ profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( qcnt == qlabel.size() ) ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] bool a1 = i2->second; ^~ profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] bool sawNamedAllele = false; ^~~~~~~~~~~~~~ profile.cpp:629:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::__cxx11::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i NList::deparseStringList(std::__cxx11::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i > NList::tokenize(std::__cxx11::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( s[i]== range_char && i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if ( i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp In file included from helper.h:24, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g = 0; g < nullModel.group.size(); g++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; g::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g2=0; g2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( g < nullModel.group.size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s < conditioner.size(); s++) ~~^~~~~~~~~~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< tok.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < tok.size() ; i++ ) ~~^~~~~~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( mapping.size() != H->ns + H->nh ) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< lst.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1142:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; g< model.group.size(); g++) ~^~~~~~~~~~~~~~~~~~~~ whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c < P->conditioner.size(); c++) ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l&, ChapModel&)': whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h < m.group.size(); h++) ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 simul.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] double gh_11_12 = h11*h12; ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~ gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] bool fatal = false; ^~~~~ gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:678:36: warning: variable 'is' set but not used [-Wunused-but-set-variable] map::iterator is = idescription.find(*ir); ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s2=s1+1; s2::iterator i2 = isection.begin(); ^~ cnv.cpp:1103:36: warning: variable 'il' set but not used [-Wunused-but-set-variable] map::iterator il = segmentLength.find(t); ^~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] int nseg = 1; ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] 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] int cnt = 0; ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] noCovar == true; ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] indivPair p = ic->first; ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ cnv.cpp: In member function 'void Plink::processCNVList()': cnv.cpp:1500:13: warning: 'cdet.CInfo::lstart' may be used uninitialized in this function [-Wmaybe-uninitialized] CInfo cdet; ^~~~ cnv.cpp:1500:13: warning: 'cdet.CInfo::lstop' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:19: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< ari->second.size(); l+=2) ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] long int nfound = 0; ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:221:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 setscreen.cpp In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != cols ) ~~~~~~~~~~~~~~^~~~~~~ setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < pS->snpset.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < snpset[j].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 In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::__cxx11::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:63:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; gvalues.size(); g++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::map >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( found != matchTemplate.size() ) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] bool match = true; ^~~~~ idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < mask.size() ; i++) ~~^~~~~~~~~~~~~ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] vector & jo = jointOrder[j]; ^~ idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:547:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:553:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] bool seenJoint = true; ^~~~~~~~~ idhelp.cpp:584:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:594:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:678:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:747:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] set & jf = jointField[j]; ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != file->uniqFieldCount ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( v->value.size() + 3 > myField->width ) ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] IDGroup * group = idgroup[g]; ^~~~~ idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0; k < (*i0)->values.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; zvalues.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z<(*i0)->values.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < targetFields.size(); f++) ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size(); i++) ~~^~~~~~~~~~~~~~~ idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= maxfield ) ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < thisGroup->values.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s< par::idhelp_match_string.size(); s+=2) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < fieldNames.size(); f++) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:22: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( maxF >= tok.size() ) ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int v=0; vvalues.size(); v++) ~^~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] bool jointQuery = id.find("+") != string::npos; ^~~~~~~~~~ idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k = 0 ; k < thisLine.size() ; k++ ) ~~^~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 hapglm.cpp In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int t = 0 ; t < tokens.size() ; t++) ~~^~~~~~~~~~~~~~~ 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 In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] int nsnps = toPosition - fromPosition + 1; ^~~~~ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] int numStrong = 0; ^~~~~~~~~ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] int numRec = 0; ^~~~~~ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] int numInGroup = 0; ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k0 ) loglike1 += knownBA * log( pB1 ); ~~~^~~~~~~ blox.cpp:505:10: warning: 'pB1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ blox.cpp:503:10: warning: 'pA2' may be used uninitialized in this function [-Wmaybe-uninitialized] double pA = pA1 + pA2; ^~ blox.cpp:505:10: warning: 'pA1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp In file included from helper.h:24, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 dosage.cpp In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int q = 0 ; q < qthresh.size() ; q++) ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < vzin.size() ; f++ ) ~~^~~~~~~~~~~~~ dosage.cpp:581:20: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tok.size() < firstCol ) ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=firstCol; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < personMap[f].size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:24: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != expected[f] ) dosage.cpp:989:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int q=0; qgetStatistic() : 0; ^~~~~~~~~ dosage.cpp:1252:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( o->second != dosageFilename_all.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++qq == qthresh.size() ) ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] int geno_field = a2_field + skip2 + 1; ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:9: warning: unused variable 'include' [-Wunused-variable] bool include = false; ^~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor 'Alleles::Alleles(std::__cxx11::string, int, int, std::__cxx11::string, std::__cxx11::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] int bp; ^~ metaanal.cpp:44:10: warning: 'std::__cxx11::string Alleles::a1' [-Wreorder] string a1; ^~ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] Alleles(string name, int chr, int bp, string a1, string a2) ^~~~~~~ metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < par::meta_files.size() ; f++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != fsize ) ~~~~~~~~~~~~~~^~~~~~~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] int pval_column = -1; ^~~~~~~~~~~ metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] { 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] { 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] 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] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] int ct = data->length(); ^~ r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rCov; ^~~~ r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rS; ^~ r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rP; ^~ r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rN; ^~ r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rc; ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.h:42, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] #warning using little endian based on information from endian.h ^~~~~~~ In file included from Rconnection.cpp:30: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { 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] { 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] 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] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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] 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' if (host) free(host); host=0; ^~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp 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 fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install 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_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/plink/usr/lib/debian-med/bin/plink was not linked against libdl.so.2 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-2_arm64.deb'. dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../plink_1.07+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/2710/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2710/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/2710 and its subdirectories I: Current time: Thu Oct 14 05:55:06 +14 2021 I: pbuilder-time-stamp: 1634140506