Diff of the two buildlogs: -- --- b1/build.log 2021-08-23 04:47:49.749868822 +0000 +++ b2/build.log 2021-08-23 05:08:01.092828585 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 24 22:58:05 -12 2022 -I: pbuilder-time-stamp: 1664103485 +I: Current time: Mon Aug 23 18:47:55 +14 2021 +I: pbuilder-time-stamp: 1629694075 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./plink_1.07+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.H0PZ6Dg6/trustedkeys.kbx': General error -gpgv: Signature made Sat Jan 4 20:03:31 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.H3WvZBSp/trustedkeys.kbx': General error +gpgv: Signature made Sun Jan 5 22:03:31 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,169 @@ dpkg-source: info: applying Fix_spelling_error.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24211/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/23291/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-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/23291/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/23291/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges: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]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + 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='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='24211' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=23291 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.JDnTHwokSx/pbuilderrc_MfNW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JDnTHwokSx/b1 --logfile b1/build.log plink_1.07+dfsg-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.JDnTHwokSx/pbuilderrc_kCOg --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JDnTHwokSx/b2 --logfile b2/build.log plink_1.07+dfsg-3.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 codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/24211/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 23 18:48 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/23291/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +263,7 @@ Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] -Fetched 18.1 MB in 0s (49.7 MB/s) +Fetched 18.1 MB in 4s (4504 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) @@ -378,7 +412,8 @@ fakeroot is already the newest version (1.25.3-1.1). 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" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plink_1.07+dfsg-3_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-3_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -415,136 +450,55 @@ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp g++ -Wall -g -fdebug-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 input.cpp:24: +In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from binput.cpp:23: +In file included from genome.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:516:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 516 | if ( i == include.size() ) - | ~~^~~~~~~~~~~~~~~~~ -input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 521 | if ( i > include.size()) - | ~~^~~~~~~~~~~~~~~~ -input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 545 | if ( gn != 2 * include.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~~ -input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 579 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 611 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 631 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 261 | while (s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 695 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'bool Plink::readClusterFile(bool)': -input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 787 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 817 | if (tokens.size() < 2+par::mult_clst) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -input.cpp:821:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 821 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 897 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 927 | for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 961 | else if ( ccount != tokens.size() ) - | ~~~~~~~^~~~~~~~~~~~~~~~ -input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 965 | if (tokens.size() < 2+par::mult_pheno) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1043 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1064 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from input.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from binput.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::makePhenotype()': -input.cpp:1208:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1208 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1232 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp:1256:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1256 | if (tokens.size() < 2+par::mult_covar) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -input.cpp:1261:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1261 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1374 | else if (tokens.size() != par::clist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +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] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': +genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] + 99 | int geno_nm = 0; + | ^~~~~~~ +genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] + 81 | double tothet = 0; + | ^~~~~~ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 309 | for (int i=0; i&, std::vector&, std::vector >&)': -stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] - 458 | int m,l,iter,i,k; - | ^ tinput.cpp:591:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 591 | if ( c > sample.size()) | ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 603 | if ( gn != 2 * sample.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::calcFst()': +genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] + 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); + | ^~ +binput.cpp: In member function 'void Plink::readBinData()': +binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 351 | while (c<7 && s&, std::vector&, std::vector >&)': +stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] + 458 | int m,l,iter,i,k; + | ^ +binput.cpp:398:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readData()': +input.cpp:516:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 516 | if ( i == include.size() ) + | ~~^~~~~~~~~~~~~~~~~ +input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 521 | if ( i > include.size()) + | ~~^~~~~~~~~~~~~~~~ +genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': +genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 1067 | if ( (!par::silent ) && c==c2 || c==np) + | ~~~~~~~~~~~~~~~~^~~~~~~~ +input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 545 | if ( gn != 2 * include.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~~ +input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 579 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 611 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 631 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1227 | for (int i=0;i > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] 906 | const double eps = 1e-12; | ^~~ -input.cpp:1519:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1572 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1477 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1483 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1515 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -input.cpp:1599:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 1599 | else if (tokens.size() != par::plist_number + 2 ) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1521 | for (int c = 0 ; c < keep.size(); c++) - | ~~^~~~~~~~~~~~~ -input.cpp:1602:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1531 | for (int i = 0; i < v.size(); i++) - | ~~^~~~~~~~~~ -input.cpp:1745:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1792 | for (int i=0; i&, std::vector&, int&)': -input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2225 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readFamFile(std::string)': -input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2419 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -input.cpp:2453:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2471 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': -genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] - 99 | int geno_nm = 0; - | ^~~~~~~ -genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] - 81 | double tothet = 0; - | ^~~~~~ +genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] + 1189 | int win_end = win_start + par::prune_ld_win; + | ^~~~~~~ helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 58 | for (int i=0; ifreq * ( 1 - locus[l]->freq ); - | ^~ helper.cpp: In function 'std::string displayLine(std::vector >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 90 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ +input.cpp: In member function 'void Plink::readSet()': +input.cpp:695:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 695 | for (int i=0; i&)': helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ -genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': -genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] - 843 | double e10 = E10*S; - | ^~~ -genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] - 844 | double e20 = E20*S; - | ^~~ -genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] - 848 | double e21 = E21*S; - | ^~~ -genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': -genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 1067 | if ( (!par::silent ) && c==c2 || c==np) - | ~~~~~~~~~~~~~~~~^~~~~~~~ -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] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -genome.cpp: In member function 'void Plink::pruneLD()': -genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1477 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1483 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1515 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1521 | for (int c = 0 ; c < keep.size(); c++) + | ~~^~~~~~~~~~~~~ +stats.cpp: In function 'matrix_t vec2diag(vector_t&)': +stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1531 | for (int i = 0; i < v.size(); i++) + | ~~^~~~~~~~~~ +input.cpp: In member function 'bool Plink::readClusterFile(bool)': +input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 787 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 817 | if (tokens.size() < 2+par::mult_clst) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +input.cpp:821:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 821 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 897 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 927 | for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 961 | else if ( ccount != tokens.size() ) + | ~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 965 | if (tokens.size() < 2+par::mult_pheno) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1043 | for (int i=0; i > CArgs::value(std::string, int)': helper.cpp:267:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) @@ -753,6 +698,9 @@ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); | ~~~~~~~~~^~~~ +input.cpp:1064:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1064 | for (int i=0; i > parse2str(std::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 306 | for (int i=0 ; i < s.length() ; i++) @@ -767,10 +715,36 @@ helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 323 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1208 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1232 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1256 | if (tokens.size() < 2+par::mult_covar) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +input.cpp:1261:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1261 | for (int i0=0; i0 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 461 | for (int i=1; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1374 | else if (tokens.size() != par::clist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'void summaryBasics(Plink&)': helper.cpp:595:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ +In file included from plink.cpp:40: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) @@ -824,6 +803,22 @@ helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1040 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1572 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 1599 | else if (tokens.size() != par::plist_number + 2 ) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +input.cpp:1602:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1602 | for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1273 | if (locus[l]->name.length() > par::pp_maxsnp) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +input.cpp:1745:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1764 | for (int c=0; c vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1391 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1792 | for (int i=0; i&, std::vector&, int&)': +input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2225 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readFamFile(std::string)': +input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2471 | for (int i=0; i&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; @@ -887,11 +938,19 @@ helper.cpp:2638:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2106 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2366 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2671 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2722 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2756 | for (int j=1; j::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ -plink.cpp: In function 'int main(int, char**)': -plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 763 | par::make_founders && - | ~~~~~~~~~~~~~~~~~~~^~ - 764 | !par::built_families) - | ~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; @@ -935,19 +983,6 @@ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] 3329 | int nextChromosome; | ^~~~~~~~~~~~~~ -plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2106 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2366 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp 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] @@ -1074,6 +1108,7 @@ multi.cpp:155:8: warning: unused variable 'is1zero' [-Wunused-variable] 155 | bool is1zero = IBDg.z1 < EPS ? true : false; | ^~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from helper.h:24, from cluster.cpp:23: @@ -1109,7 +1144,6 @@ cluster.cpp:786:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 190 | for (int i1=0; i1 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1257,15 +1292,15 @@ output.cpp:553:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::keep2SetsForGenome()': -output.cpp:788:7: warning: unused variable 'n_removed' [-Wunused-variable] - 788 | int n_removed = deleteIndividuals(del); - | ^~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1331,11 +1364,25 @@ assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp +output.cpp: In member function 'void Plink::display_pairList()': +output.cpp:144:65: warning: 'i1' may be used uninitialized in this function [-Wmaybe-uninitialized] + 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " + | ^ +output.cpp:145:65: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized] + 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " + | ^ In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from prephap.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 146 | for (int e=0;e >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1378,13 +1420,6 @@ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -output.cpp: In member function 'void Plink::display_pairList()': -output.cpp:144:65: warning: 'i1' may be used uninitialized in this function [-Wmaybe-uninitialized] - 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " - | ^ -output.cpp:145:65: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized] - 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " - | ^ prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 470 | for (int s=0;s Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1109:61: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] 1109 | pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); | ~~~~~^~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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 phase.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] @@ -1436,11 +1471,6 @@ phase.cpp:678:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 678 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::map, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ @@ -1467,6 +1497,11 @@ phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ +In file included from trio.cpp:23: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 91 | for (int c=0; ckid.size(); c++) @@ -1571,6 +1606,12 @@ tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from perm.h:17, + from sharing.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 412 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ @@ -1590,32 +1631,102 @@ tdt.cpp:776:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp +perm.cpp: In member function 'void Perm::permuteInCluster()': +perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 199 | for(int i=0; i&, std::vector&)': +perm.cpp:273:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 273 | for (int j=0;j< P.pS->snpset[l].size();j++) + | ~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from genepi.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': -sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 102 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +genepi.cpp: In function 'double C(int, double, double)': +genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] + 78 | } + | ^ +genepi.cpp: In function 'long double pillai(int, int, int, double)': +genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] + 169 | } + | ^ +genepi.cpp: In member function 'void Plink::driverSCREEPI()': +genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 334 | for (int s=0; s >&, Set&, Plink&)': +genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 489 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 497 | for (int l=0; l >&, Set&, Plink&)': +genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1025 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1033 | for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': +genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] + 1198 | bool casewise_deletion = false; + | ^~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 37 | for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -perm.cpp: In member function 'void Perm::permuteInCluster()': -perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 199 | for(int i=0; i&, std::vector&)': -perm.cpp:273:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 273 | for (int j=0;j< P.pS->snpset[l].size();j++) - | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from genepi.cpp:24: + from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -genepi.cpp: In function 'double C(int, double, double)': -genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] - 78 | } - | ^ -genepi.cpp: In function 'long double pillai(int, int, int, double)': -genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] - 169 | } - | ^ -genepi.cpp: In member function 'void Plink::driverSCREEPI()': -genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 334 | for (int s=0; s >&, Set&, Plink&)': -genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 489 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 497 | for (int l=0; l >&, Set&, Plink&)': -genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1025 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1033 | for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': -genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] - 1198 | bool casewise_deletion = false; - | ^~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp In file included from perm.h:17, - from mh.cpp:20: + from genedrop.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +genedrop.cpp: In member function 'void Perm::preGeneDrop()': +genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 64 | for (int i=0; i&, std::vector&, std::vector&, std::map&)': +genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 340 | for (int k=0; kkids.size(); k++) + | ~^~~~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-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 -genedrop.cpp: In member function 'void Perm::preGeneDrop()': -genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 64 | for (int i=0; i&, std::vector&, std::vector&, std::map&)': -genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 340 | for (int k=0; kkids.size(); k++) - | ~^~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -1854,6 +1889,11 @@ merge.cpp:426:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 426 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ merge.cpp:722:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ @@ -1869,8 +1909,8 @@ merge.cpp:842:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 842 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) @@ -1882,12 +1922,6 @@ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 173 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 85 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -1938,7 +1973,6 @@ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp In file included from 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] @@ -1954,7 +1988,16 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp +merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': +merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] + 1103 | if (write) + | ^~ +In file included from helper.h:24, + from webcheck.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 93 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 328 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 117 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -linear.cpp: In member function 'virtual void LinearModel::pruneY()': -linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) @@ -2047,13 +2073,31 @@ qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] 639 | int tc = 0; | ^~ +g++ -Wall -g -fdebug-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 helper.h:24, + from linear.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +linear.cpp: In member function 'virtual void LinearModel::pruneY()': +linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from bmerge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp -g++ -Wall -g -fdebug-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 bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] 90 | long int inc; @@ -2091,20 +2135,11 @@ bmerge.cpp:883:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 883 | for (int i=0; i, int>&)': -merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] - 1103 | if (write) - | ^~ In file included from mishap.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from parse.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from 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] @@ -2125,7 +2160,6 @@ | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-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 g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp -g++ -Wall -g -fdebug-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 legacy.cpp:22: options.h: In member function 'void OptionSet::display()': @@ -2172,7 +2206,6 @@ legacy.cpp:480:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 480 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 695 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-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 homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ @@ -2198,12 +2232,6 @@ homozyg.cpp:861:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 861 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ -In file included from helper.h:24, - from segment.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) @@ -2226,6 +2254,13 @@ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp +In file included from helper.h:24, + from segment.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) @@ -2327,26 +2362,26 @@ 613 | double maxVIF = 0; | ^~~~~~ g++ -Wall -g -fdebug-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 +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp +g++ -Wall -g -fdebug-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 dcdflib.cpp In file included from helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i *xn)) goto S160; | ~~~~~~~~~~~~^~~~~~~~~~~ +logistic.cpp: In member function 'double LogisticModel::getPValue()': +logistic.cpp:327:8: warning: unused variable 'okay' [-Wunused-variable] + 327 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; + | ^~~~ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; @@ -2403,51 +2438,27 @@ glm.cpp:423:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 423 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp -elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': -elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 493 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': -elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 609 | for (int l=0; l< original.size(); l++) - | ~^~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': -elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] - 654 | const double pthresh = 0.01; - | ^~~~~~~ -elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] - 655 | bool one_sided = true; - | ^~~~~~~~~ -elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] - 707 | int srange_cnt = 0; - | ^~~~~~~~~~ -elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] - 708 | bool inRange = false; - | ^~~~~~~ -elf.cpp: In member function 'void Plink::displayRareRange()': -elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 895 | for (int i = 0 ; i < tokens.size() ; i++) - | ~~^~~~~~~~~~~~~~~ -elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 939 | if ( tokens.size() != ncol ) - | ~~~~~~~~~~~~~~^~~~~~~ In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': +elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 493 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 609 | for (int l=0; l< original.size(); l++) + | ~^~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': +elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] + 654 | const double pthresh = 0.01; + | ^~~~~~~ +elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] + 655 | bool one_sided = true; + | ^~~~~~~~~ +elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] + 707 | int srange_cnt = 0; + | ^~~~~~~~~~ +elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] + 708 | bool inRange = false; + | ^~~~~~~ +elf.cpp: In member function 'void Plink::displayRareRange()': +elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 895 | for (int i = 0 ; i < tokens.size() ; i++) + | ~~^~~~~~~~~~~~~~~ +elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 939 | if ( tokens.size() != ncol ) + | ~~~~~~~~~~~~~~^~~~~~~ g++ -Wall -g -fdebug-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 helper.h:24, from fisher.cpp:17: @@ -2562,12 +2597,12 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) @@ -2591,7 +2626,6 @@ 209 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 289 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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:18: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 314 | for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp proxy.cpp:1332:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2668,23 +2716,10 @@ proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] 1448 | int t1=0; | ^~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ -In file included from pdriver.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from pdriver.cpp:18: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2702,6 +2737,7 @@ haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1154:8: warning: 'p_gcnt' may be used uninitialized in this function [-Wmaybe-uninitialized] 1154 | ++(*p_gcnt); @@ -2709,14 +2745,13 @@ elf.cpp:1165:5: warning: 'p_cnt' may be used uninitialized in this function [-Wmaybe-uninitialized] 1165 | ++(*p_cnt); | ^~~~~~~~~~ -g++ -Wall -g -fdebug-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 g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from 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] @@ -2788,6 +2823,7 @@ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1225 | for (int z = 0; z < hap1[p1].size(); z++) @@ -2808,7 +2844,6 @@ haplohelper.cpp:1477:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1477 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) @@ -2818,11 +2853,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from genogroup.cpp:23: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2881,6 +2911,11 @@ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -2915,6 +2950,7 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) @@ -2933,7 +2969,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': @@ -2956,12 +2991,26 @@ clumpld.cpp:174:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from genoerr.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ clumpld.cpp:201:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 201 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from genoerr.cpp:27: +genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': +genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) @@ -2972,9 +3021,39 @@ clumpld.cpp:520:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ +In file included from genoerr.cpp:28: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 157 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ +genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 189 | for( int a = 0; a < posshap1.size(); a++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 190 | for( int b = 0; b < posshap2.size(); b++ ) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 225 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 315 | for (int z = 0; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 328 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 347 | for (int z = 0; z < new_hap1.size(); z++) + | ~~^~~~~~~~~~~~~~~~~ +genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 358 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -3019,52 +3098,7 @@ em.cpp:166:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 166 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from genoerr.cpp:27: -genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': -genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 189 | for( int a = 0; a < posshap1.size(); a++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 190 | for( int b = 0; b < posshap2.size(); b++ ) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 225 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 315 | for (int z = 0; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 328 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 347 | for (int z = 0; z < new_hap1.size(); z++) - | ~~^~~~~~~~~~~~~~~~~ -genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 358 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3079,6 +3113,7 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -3130,19 +3165,12 @@ | ~^~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp g++ -Wall -g -fdebug-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 nlist.cpp +g++ -Wall -g -fdebug-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 profile.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from nlist.h:21, - from nlist.cpp:17: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-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 profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; @@ -3168,6 +3196,27 @@ profile.cpp:421:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ +profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': +profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] + 480 | bool a1 = i2->second; + | ^~ +profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] + 525 | bool sawNamedAllele = false; + | ^~~~~~~~~~~~~~ +profile.cpp:629:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': +profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 38 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 124 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 151 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ -profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': -profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] - 480 | bool a1 = i2->second; - | ^~ -profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] - 525 | bool sawNamedAllele = false; - | ^~~~~~~~~~~~~~ -profile.cpp:629:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': -profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from simul.cpp:16: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': -simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] - 172 | double gh_11_12 = h11*h12; - | ^~~~~~~~ -simul.cpp: In member function 'void Plink::simulateSNPs()': -simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 679 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) @@ -3283,7 +3291,6 @@ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 962 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1425 | for (int h=0; h < m.group.size(); h++) @@ -3335,7 +3343,34 @@ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from simul.cpp:16: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp +simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': +simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] + 172 | double gh_11_12 = h11*h12; + | ^~~~~~~~ +simul.cpp: In member function 'void Plink::simulateSNPs()': +simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 679 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1211 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 556 | for (int i=0; i&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; @@ -3492,7 +3527,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3503,6 +3537,7 @@ qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from helper.h:24, from cnvqt.cpp:22: @@ -3510,12 +3545,13 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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 cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) @@ -3536,12 +3572,23 @@ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp +In file included from idhelp.cpp:18: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp +g++ -Wall -g -fdebug-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 setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp -In file included from idhelp.cpp:18: -idhelp.h: In member function 'void IDGroup::display()': -idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) @@ -3576,6 +3609,7 @@ idhelp.cpp:63:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 63 | for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) @@ -3590,12 +3624,6 @@ idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from tag.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -3667,12 +3695,6 @@ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from hapglm.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ @@ -3755,11 +3777,6 @@ idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1551 | for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1631 | for (int i=0; i > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2167 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:2168:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2168 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from tag.cpp:24: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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 helper.h:24, + from hapglm.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from lookup2.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from hapglm.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) @@ -3911,13 +3946,13 @@ | ^~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from helper.h:24, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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 blox.cpp:569:41: warning: 'pB2' may be used uninitialized in this function [-Wmaybe-uninitialized] 569 | if ( pB1>0 ) loglike1 += knownBA * log( pB1 ); | ~~~^~~~~~~ @@ -3944,11 +3979,6 @@ dosage.cpp:110:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ -In file included from annot.cpp:20: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 513 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 83 | for (int j=1; jgetStatistic() : 0; | ^~~~~~~~~ @@ -3985,6 +4011,15 @@ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] 190 | int geno_field = a2_field + skip2 + 1; | ^~~~~~~~~~ +In file included from annot.cpp:20: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +annot.cpp: In member function 'void Plink::annotateFile()': +annot.cpp:83:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 149 | for (int i=0; i=nel)?0:cont[i]; } + | ~^~~~~ +Rconnection.h: In member function 'void Rstrings::decode()': +Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] + 245 | while (i < len) { if (!c[i]) nel++; i++; } + | ~~^~~~~ +Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 249 | while (i < nel) { + | ~~^~~~~ +Rconnection.cpp: At global scope: +Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ + | ^~~~~~~~~~~~~~ +Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': +Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 567 | if (host) free(host); host=0; + | ^~ +Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 567 | if (host) free(host); host=0; + | ^~~~ 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] @@ -4053,37 +4119,6 @@ metaanal.cpp:300:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from Rconnection.cpp:30: -Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': -Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 203 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': -Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 206 | { name=""; fix_content(); } - | ^~ -Rconnection.h: In member function 'char* Rstrings::stringAt(int)': -Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } - | ~^~~~~ -Rconnection.h: In member function 'void Rstrings::decode()': -Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] - 245 | while (i < len) { if (!c[i]) nel++; i++; } - | ~~^~~~~ -Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 249 | while (i < nel) { - | ~~^~~~~ -Rconnection.cpp: At global scope: -Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ - | ^~~~~~~~~~~~~~ -Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': -Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 567 | if (host) free(host); host=0; - | ^~ -Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 567 | if (host) free(host); host=0; - | ^~~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] 253 | int pval_column = -1; | ^~~~~~~~~~~ @@ -4192,12 +4227,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/23291/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/23291/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/24211 and its subdirectories -I: Current time: Sat Sep 24 23:10:47 -12 2022 -I: pbuilder-time-stamp: 1664104247 +I: removing directory /srv/workspace/pbuilder/23291 and its subdirectories +I: Current time: Mon Aug 23 19:07:59 +14 2021 +I: pbuilder-time-stamp: 1629695279