Diff of the two buildlogs: -- --- b1/build.log 2021-09-07 01:56:47.438405602 +0000 +++ b2/build.log 2021-09-07 02:14:24.236461312 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 6 13:44:24 -12 2021 -I: pbuilder-time-stamp: 1630979064 +I: Current time: Tue Sep 7 15:57:45 +14 2021 +I: pbuilder-time-stamp: 1630979865 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.iZDp94I7/trustedkeys.kbx': General error -gpgv: Signature made Sat Jan 4 20:03:31 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.QLzTYsm7/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/24315/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/23815/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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/23815/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/23815/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='984683aa46864fcda60a1856c16bc74a' - 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='24315' - PS1='# ' - PS2='> ' + INVOCATION_ID=f12b612382ca428eb6762272329ce002 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=23815 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.dFbkXBOBAQ/pbuilderrc_PI9Z --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dFbkXBOBAQ/b1 --logfile b1/build.log plink_1.07+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.dFbkXBOBAQ/pbuilderrc_IzO9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dFbkXBOBAQ/b2 --logfile b2/build.log plink_1.07+dfsg-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt32b 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:25 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 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/24315/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 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 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 7 15:58 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/23815/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 armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] -Fetched 17.9 MB in 2s (7515 kB/s) +Fetched 17.9 MB in 2s (8975 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 ... 19398 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: Name or service not known +I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-3_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -390,7 +425,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/plink-1.07+dfsg' @@ -405,21 +440,32 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-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' FORCE_DYNAMIC=1 - make -j3 "INSTALL=install --strip-program=true" "CXXFLAGS=-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" FORCE_DYNAMIC=1 + make -j4 "INSTALL=install --strip-program=true" "CXXFLAGS=-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" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/plink-1.07+dfsg' 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 plink.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 options.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 input.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 binput.cpp In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from plink.cpp:28: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from 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 '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 '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 'unsigned int'} [-Wsign-compare] 516 | if ( i == include.size() ) @@ -427,11 +473,6 @@ input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 521 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 545 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ @@ -455,6 +496,11 @@ input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 787 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ @@ -468,12 +514,28 @@ input.cpp:927:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 927 | for ( int i=2; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 157 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 176 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 186 | for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] 961 | else if ( ccount != tokens.size() ) | ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +binput.cpp:261:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 261 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] 1037 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1064 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 339 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 351 | while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] + 398 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::makePhenotype()': input.cpp:1208:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1208 | for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from plink.cpp:40: +idhelp.h: In member function 'void IDGroup::display()': +idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 196 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 1519 | for (int c=0; c >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1602 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1745 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] 2419 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2453 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 196 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] 2106 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2366 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -binput.cpp: In member function 'void Plink::readBinData()': -binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 126 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 157 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 176 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 186 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 261 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 339 | while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 351 | while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] - 398 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from input.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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 tinput.cpp In file included from /usr/include/c++/10/algorithm:62, from binput.cpp:19: /usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -657,56 +682,6 @@ 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2707:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2707 | std::__insertion_sort(__first, __first + __chunk_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2710 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2685 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2687 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2688 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2693 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2694 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2685 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2687 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2688 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2693 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2694 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2710 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, @@ -759,34 +734,6 @@ /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1318 | __rotate(_RandomAccessIterator __first, - | ^~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2488 | __merge_without_buffer(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1434 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1435 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2529:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2529 | std::__merge_without_buffer(__first, __first_cut, __new_middle, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2530 | __len11, __len22, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2531:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2531 | std::__merge_without_buffer(__new_middle, __second_cut, __last, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2532 | __len1 - __len11, __len2 - __len22, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2488 | __merge_without_buffer(_BidirectionalIterator __first, @@ -1056,6 +1003,315 @@ | ~~~~~~~~~~~~~~~~~~ 2787 | __comp); | ~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +tinput.cpp: In member function 'void Plink::readTransposedData()': +tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) + | ~~~~~~~~~~^~~~~~~~~~~~~~ +tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 271 | for(int l=0; l < locus.size(); l++) + | ~~^~~~~~~~~~~~~~ +tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 309 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 591 | if ( c > sample.size()) + | ~~^~~~~~~~~~~~~~~ +tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 603 | if ( gn != 2 * sample.size() ) + | ~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from binput.cpp:22: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:62, + from /usr/include/c++/10/algorithm:62, + from binput.cpp:19: +/usr/include/c++/10/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, std::_Temporary_buffer<_ForwardIterator, _Tp>::size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': +/usr/include/c++/10/bits/stl_tempbuf.h:257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 257 | _Temporary_buffer<_ForwardIterator, _Tp>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from binput.cpp:19: +/usr/include/c++/10/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2389 | __rotate_adaptive(_BidirectionalIterator1 __first, + | ^~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1434 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1435 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2427 | __merge_adaptive(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2472:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2472 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2473 | __len1 - __len11, __len22, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2474 | __buffer_size); + | ~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2475:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2475 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2476 | __len22, __buffer, __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2477:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2477 | std::__merge_adaptive(__new_middle, __second_cut, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2478 | __len1 - __len11, + | ~~~~~~~~~~~~~~~~~ + 2479 | __len2 - __len22, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2480 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2744 | __stable_sort_adaptive(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2753:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2753 | std::__stable_sort_adaptive(__first, __middle, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2754 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2755:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2755 | std::__stable_sort_adaptive(__middle, __last, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2756 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2760:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2760 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2761:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2761 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2763:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2763 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2764 | _Distance(__middle - __first), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2765 | _Distance(__last - __middle), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2766 | __buffer, __buffer_size, + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 2767 | __comp); + | ~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from input.cpp:18: +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from binput.cpp:22: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readBinData()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from binput.cpp:19: +/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); + | ^~~~~ +/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5035 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5038 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); + | ^~~~~ +/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5035 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5038 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from tinput.cpp:19: +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2707:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2707 | std::__insertion_sort(__first, __first + __chunk_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2710 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2685 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2687 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2688 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2693 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2694 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2685 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2687 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2688 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2693 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2694 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2710 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1318 | __rotate(_RandomAccessIterator __first, + | ^~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2707:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2707 | std::__insertion_sort(__first, __first + __chunk_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2710 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2685 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2687 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2688 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2693 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2694 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2685 | __result = std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2686 | __first + __step_size, + | ~~~~~~~~~~~~~~~~~~~~~~ + 2687 | __first + __two_step, + | ~~~~~~~~~~~~~~~~~~~~~ + 2688 | __result, __comp); + | ~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2693 | std::__move_merge(__first, __first + __step_size, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2694 | __first + __step_size, __last, __result, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2710 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2488 | __merge_without_buffer(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1434 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1435 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2529:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2529 | std::__merge_without_buffer(__first, __first_cut, __new_middle, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2530 | __len11, __len22, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2531:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2531 | std::__merge_without_buffer(__new_middle, __second_cut, __last, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2532 | __len1 - __len11, __len2 - __len22, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1318 | __rotate(_RandomAccessIterator __first, + | ^~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2773:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2773 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -1304,271 +1560,6 @@ | ~~~~~~~~~~~~~~~~~~ 2787 | __comp); | ~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from binput.cpp:22: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:62, - from /usr/include/c++/10/algorithm:62, - from binput.cpp:19: -/usr/include/c++/10/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, std::_Temporary_buffer<_ForwardIterator, _Tp>::size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': -/usr/include/c++/10/bits/stl_tempbuf.h:257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 257 | _Temporary_buffer<_ForwardIterator, _Tp>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from binput.cpp:19: -/usr/include/c++/10/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2389 | __rotate_adaptive(_BidirectionalIterator1 __first, - | ^~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1434 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1435 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2427 | __merge_adaptive(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2472:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2472 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2473 | __len1 - __len11, __len22, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2474 | __buffer_size); - | ~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2475:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2475 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2476 | __len22, __buffer, __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2477:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2477 | std::__merge_adaptive(__new_middle, __second_cut, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2478 | __len1 - __len11, - | ~~~~~~~~~~~~~~~~~ - 2479 | __len2 - __len22, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2480 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2744 | __stable_sort_adaptive(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2753:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2753 | std::__stable_sort_adaptive(__first, __middle, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2754 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2755:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2755 | std::__stable_sort_adaptive(__middle, __last, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2756 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2760:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2760 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2761:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2761 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2763:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2763 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2764 | _Distance(__middle - __first), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2765 | _Distance(__last - __middle), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2766 | __buffer, __buffer_size, - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 2767 | __comp); - | ~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from binput.cpp:22: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readBinData()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from binput.cpp:19: -/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); - | ^~~~~ -/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5035 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5038 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); - | ^~~~~ -/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5035 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5038 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from input.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from input.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readSegmentFile(std::ifstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readSegmentFileMinimal(std::ifstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 tinput.cpp -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from input.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -tinput.cpp: In member function 'void Plink::readTransposedData()': -tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 161 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 218 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 246 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 256 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) - | ~~~~~~~~~~^~~~~~~~~~~~~~ -tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 271 | for(int l=0; l < locus.size(); l++) - | ~~^~~~~~~~~~~~~~ -tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 309 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 591 | if ( c > sample.size()) - | ~~^~~~~~~~~~~~~~~ -tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 603 | if ( gn != 2 * sample.size() ) - | ~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:62, - from /usr/include/c++/10/algorithm:62, - from input.cpp:18: -/usr/include/c++/10/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, std::_Temporary_buffer<_ForwardIterator, _Tp>::size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': -/usr/include/c++/10/bits/stl_tempbuf.h:257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 257 | _Temporary_buffer<_ForwardIterator, _Tp>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from tinput.cpp:19: -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2707:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2707 | std::__insertion_sort(__first, __first + __chunk_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2710 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2685 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2687 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2688 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2693 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2694 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2685:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2685 | __result = std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2686 | __first + __step_size, - | ~~~~~~~~~~~~~~~~~~~~~~ - 2687 | __first + __two_step, - | ~~~~~~~~~~~~~~~~~~~~~ - 2688 | __result, __comp); - | ~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2693 | std::__move_merge(__first, __first + __step_size, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2694 | __first + __step_size, __last, __result, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2693:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2710 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1318 | __rotate(_RandomAccessIterator __first, - | ^~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2488 | __merge_without_buffer(_BidirectionalIterator __first, @@ -1590,6 +1581,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2532 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from tinput.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2773:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2773 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -1838,13 +1836,6 @@ | ~~~~~~~~~~~~~~~~~~ 2787 | __comp); | ~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from tinput.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:62, from /usr/include/c++/10/algorithm:62, from tinput.cpp:19: @@ -1926,19 +1917,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ 2767 | __comp); | ~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from input.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'bool Plink::readMultiplePhenoFile()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 In file included from /usr/include/c++/10/vector:67, from plink.h:21, from tinput.cpp:23: @@ -1970,123 +1949,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5038 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'bool Plink::readCovListFile()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 -In file included from /usr/include/c++/10/algorithm:62, - from input.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2389 | __rotate_adaptive(_BidirectionalIterator1 __first, - | ^~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1434 | return std::__rotate(__first, __middle, __last, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1435 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2427 | __merge_adaptive(_BidirectionalIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2472:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2472 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2473 | __len1 - __len11, __len22, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2474 | __buffer_size); - | ~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2475:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2475 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2476 | __len22, __buffer, __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2477:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2477 | std::__merge_adaptive(__new_middle, __second_cut, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2478 | __len1 - __len11, - | ~~~~~~~~~~~~~~~~~ - 2479 | __len2 - __len22, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2480 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2744 | __stable_sort_adaptive(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2753:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2753 | std::__stable_sort_adaptive(__first, __middle, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2754 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2755:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2755 | std::__stable_sort_adaptive(__middle, __last, __buffer, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2756 | __buffer_size, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2760:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2760 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2761:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2761 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2763:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2763 | std::__merge_adaptive(__first, __middle, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2764 | _Distance(__middle - __first), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2765 | _Distance(__last - __middle), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 2766 | __buffer, __buffer_size, - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 2767 | __comp); - | ~~~~~~~ -In file included from /usr/include/c++/10/vector:67, +In file included from /usr/include/c++/10/vector:72, from plink.h:21, from input.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from input.cpp:18: -/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); - | ^~~~~ -/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5035 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5038 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); - | ^~~~~ -/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5035 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5038 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] @@ -2103,6 +1980,13 @@ genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); | ^~ +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from input.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readSegmentFile(std::ifstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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; @@ -2124,16 +2008,35 @@ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] 1189 | int win_end = win_start + par::prune_ld_win; | ^~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readSegmentFileMinimal(std::ifstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from input.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Locus&}; _Tp = Locus; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:62, + from /usr/include/c++/10/algorithm:62, + from input.cpp:18: +/usr/include/c++/10/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, std::_Temporary_buffer<_ForwardIterator, _Tp>::size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': +/usr/include/c++/10/bits/stl_tempbuf.h:257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 257 | _Temporary_buffer<_ForwardIterator, _Tp>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 In file included from helper.h:24, from helper.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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -input.cpp: In member function 'void Plink::readData()': -input.cpp:91:13: warning: 'PED' may be used uninitialized in this function [-Wmaybe-uninitialized] - 91 | if ( feof(PED) ) - | ~~~~^~~~~ helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 58 | for (int i=0; i >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] 218 | error("Missing an argument for "+s); @@ -2362,8 +2279,6 @@ helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': @@ -2402,6 +2317,17 @@ stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1531 | for (int i = 0; i < v.size(); i++) | ~~^~~~~~~~~~ +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 filters.cpp +/usr/include/c++/10/bits/stl_vector.h: In member function 'bool Plink::readCovListFile()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2462,24 +2388,115 @@ filters.cpp:1257:7: warning: unused variable 'tmp' [-Wunused-variable] 1257 | int tmp = deleteSNPs(del); | ^~~ -In file included from /usr/include/c++/10/vector:72, - from helper.h:18, - from helper.cpp:24: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::thinSNPs()': filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] 1277 | int x = 0; | ^ +In file included from /usr/include/c++/10/algorithm:62, + from input.cpp:18: +/usr/include/c++/10/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2389 | __rotate_adaptive(_BidirectionalIterator1 __first, + | ^~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2389:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1434:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1434 | return std::__rotate(__first, __middle, __last, + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1435 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2427 | __merge_adaptive(_BidirectionalIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2472:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2472 | = std::__rotate_adaptive(__first_cut, __middle, __second_cut, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2473 | __len1 - __len11, __len22, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2474 | __buffer_size); + | ~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2475:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2475 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2476 | __len22, __buffer, __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2477:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2477 | std::__merge_adaptive(__new_middle, __second_cut, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2478 | __len1 - __len11, + | ~~~~~~~~~~~~~~~~~ + 2479 | __len2 - __len22, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2480 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2744 | __stable_sort_adaptive(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2753:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2753 | std::__stable_sort_adaptive(__first, __middle, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2754 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2755:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2755 | std::__stable_sort_adaptive(__middle, __last, __buffer, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2756 | __buffer_size, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2760:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2760 | std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2761:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2761 | std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2763:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2763 | std::__merge_adaptive(__first, __middle, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2764 | _Distance(__middle - __first), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2765 | _Distance(__last - __middle), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 2766 | __buffer, __buffer_size, + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 2767 | __comp); + | ~~~~~~~ In file included from /usr/include/c++/10/vector:67, - from helper.h:18, - from helper.cpp:24: -/usr/include/c++/10/bits/stl_vector.h: In function 'void sizeMatrix(matrix_t&, int, int)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from plink.h:21, + from input.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from input.cpp:18: +/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); + | ^~~~~ +/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5035 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5038 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5032:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5032 | _TmpBuf __buf(__first, std::distance(__first, __last)); + | ^~~~~ +/usr/include/c++/10/bits/stl_algo.h:5035:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5035 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:5037:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 5037 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5038 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from stats.h:19, from stats.cpp:24: @@ -2508,12 +2525,30 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +input.cpp: In member function 'void Plink::readData()': +input.cpp:91:13: warning: 'PED' may be used uninitialized in this function [-Wmaybe-uninitialized] + 91 | if ( feof(PED) ) + | ~~~~^~~~~ 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 locus.cpp +In file included from /usr/include/c++/10/vector:72, + from helper.h:18, + from helper.cpp:24: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from locus.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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from helper.h:18, + from helper.cpp:24: +/usr/include/c++/10/bits/stl_vector.h: In function 'void sizeMatrix(matrix_t&, int, int)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': @@ -2592,10 +2627,6 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 -helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': -helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wmaybe-uninitialized] - 1430 | cur[maxI] = false; - | ^ In file included from helper.h:24, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -2732,13 +2763,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from cluster.cpp:19: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Neighbour; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 190 | for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] 191 | for (int i2=0; i2::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 279 | if ( elist.size() != par::cluster_mds_dim ) + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] + 242 | bool flag = svd(D,eigenvalue,eigenvector); + | ^~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from cluster.cpp:19: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Neighbour; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from cluster.cpp:19: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -2753,12 +2790,6 @@ 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -mds.cpp:279:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 279 | if ( elist.size() != par::cluster_mds_dim ) - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] - 242 | bool flag = svd(D,eigenvalue,eigenvector); - | ^~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, @@ -2768,6 +2799,10 @@ 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 +helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': +helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wmaybe-uninitialized] + 1430 | cur[maxI] = false; + | ^ In file included from /usr/include/c++/10/vector:72, from plink.h:21, from cluster.cpp:22: @@ -2784,13 +2819,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from cluster.cpp:22: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::groupGenome()': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 84 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 553 | for (int l=0; l >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 informative.cpp 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); @@ -2843,7 +2879,6 @@ output.cpp:2412:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2859,6 +2894,7 @@ informative.cpp:105:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 105 | for (int i=0;i >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'int Plink::readInformative()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from helper.h:24, + from assoc.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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::buildCluster()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); @@ -2901,28 +2947,10 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'int Plink::readInformative()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ output.cpp: In member function 'void Plink::display_indivReport()': output.cpp:69:36: warning: 'i1' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | << setw(6) << genotype(*this,i1,l) << "\n"; | ^ -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 assoc.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 helper.h:24, - from assoc.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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -2948,18 +2976,14 @@ assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from assoc.cpp:21: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': -assoc.cpp:1109:61: 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 epi.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 'unsigned int'} [-Wsign-compare] @@ -2981,6 +3005,17 @@ epi.cpp:701:11: warning: unused variable 'c' [-Wunused-variable] 701 | int c=0; | ^ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from assoc.cpp:21: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': +assoc.cpp:1109:61: 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 prephap.cpp In file included from prephap.cpp:24: options.h: In member function 'void OptionSet::display()': @@ -3008,6 +3043,16 @@ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 470 | for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 560 | for (int i=0; i >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 470 | for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 533 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 560 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 1245 | for ( int k=0; kpp->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from phase.cpp:19: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from phase.cpp:19: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::prunePhase(int)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::performAlternEM()': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 tdt.cpp In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -3255,33 +3248,59 @@ tdt.cpp:776:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from phase.cpp:19: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from phase.cpp:19: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::prunePhase(int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 sharing.cpp In file included from /usr/include/c++/10/vector:72, from tdt.cpp:18: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::performAlternEM()': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:937:41: warning: 'zt' may be used uninitialized in this function [-Wmaybe-uninitialized] 937 | double OR_upper = exp( log(OR) + zt * sqrt(1/t1+1/t2)) ; | ~~~^~~~~~~~~~~~~~~~~ -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 sharing.cpp In file included from perm.h:17, from sharing.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -3292,14 +3311,29 @@ sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 genepi.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 sets.cpp +/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] @@ -3350,11 +3384,68 @@ 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 sets.cpp +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from genepi.cpp:19: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from genepi.cpp:19: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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 perm.cpp +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from genepi.cpp:23: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from genepi.cpp:23: +/usr/include/c++/10/bits/stl_vector.h: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from genepi.cpp:19: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +In file included from perm.h:17, + from perm.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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3460,62 +3551,6 @@ sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from genepi.cpp:19: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from genepi.cpp:23: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from genepi.cpp:23: -/usr/include/c++/10/bits/stl_vector.h: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'int calcGENEPIMeanVariance(std::vector&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from genepi.cpp:19: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from sets.cpp:16: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SetSortedSNP; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -3530,80 +3565,6 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from sets.cpp:16: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 perm.cpp -genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': -genepi.cpp:805:82: warning: 'cancor1_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] - 805 | gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; - | ^ -In file included from /usr/include/c++/10/algorithm:62, - from genepi.cpp:19: -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from sets.cpp:18: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from sets.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Set::profileTestScore()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from perm.h:17, - from perm.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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Set::profileTestSNPInformation(int, double)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 144 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from sets.cpp:16: -/usr/include/c++/10/bits/stl_algo.h: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from perm.cpp:15: @@ -3676,6 +3621,38 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': +genepi.cpp:805:82: warning: 'cancor1_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] + 805 | gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; + | ^ +In file included from /usr/include/c++/10/algorithm:62, + from genepi.cpp:19: +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In member function 'bool Perm::update(std::vector&, std::vector&)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -3690,8 +3667,29 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 mh.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 genedrop.cpp +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from sets.cpp:16: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SetSortedSNP; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from sets.cpp:16: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from options.h:18, from perm.h:17, @@ -3723,23 +3721,52 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 mh.cpp +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from sets.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from sets.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Set::profileTestScore()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Set::profileTestSNPInformation(int, double)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from sets.cpp:16: +/usr/include/c++/10/bits/stl_algo.h: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 747 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1249 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] 64 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ +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 merge.cpp In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka '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 merge.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -3811,12 +3846,6 @@ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 173 | for (int s=0; s::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from merge.cpp:19: /usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -3828,12 +3857,6 @@ /usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:67, - from hotel.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In function 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, @@ -3884,6 +3907,7 @@ /usr/include/c++/10/bits/stl_algo.h:2710:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2710 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 multiple.cpp /usr/include/c++/10/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1318 | __rotate(_RandomAccessIterator __first, @@ -4160,11 +4184,36 @@ | ~~~~~~~~~~~~~~~~~~ 2787 | __comp); | ~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from hotel.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from hotel.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In function 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ^~ -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 multiple.cpp +In file included from helper.h:24, + from multiple.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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': +multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 85 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] + 131 | for (int i=0; i::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -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 haploCC.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:62, from /usr/include/c++/10/algorithm:62, from merge.cpp:19: @@ -4180,6 +4228,29 @@ /usr/include/c++/10/bits/stl_tempbuf.h:257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 257 | _Temporary_buffer<_ForwardIterator, _Tp>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from multiple.cpp:18: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from multiple.cpp:18: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from merge.cpp:19: /usr/include/c++/10/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Locus*; _Distance = int]': @@ -4194,12 +4265,14 @@ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1435 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from helper.h:24, - from multiple.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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from multiple.cpp:17: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Pair&}; _Tp = Pair; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +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 haploTDT.cpp /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2427 | __merge_adaptive(_BidirectionalIterator __first, @@ -4228,13 +4301,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2480 | __buffer_size, __comp); | ~~~~~~~~~~~~~~~~~~~~~~ -multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': -multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 85 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] - 131 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2744:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2744 | __stable_sort_adaptive(_RandomAccessIterator __first, @@ -4268,41 +4339,40 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ 2767 | __comp); | ~~~~~~~ -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from multiple.cpp:18: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from multiple.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from multiple.cpp:17: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Pair&}; _Tp = Pair; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from haploCC.cpp:24: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ +In file included from haploCC.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, int, bool)': +haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 48 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 62 | if ( ! ( haploid || X && person->sex ) ) + | ~~^~~~~~~~~~~~~~ +haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 79 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 93 | if ( ! ( haploid || X && person->sex ) ) + | ~~^~~~~~~~~~~~~~ +haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] + 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); + | ^ +haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': +haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 340 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 357 | if ( ! ( haploid || X && person->sex ) ) + | ~~^~~~~~~~~~~~~~ +haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 375 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 392 | if ( ! ( haploid || X && person->sex ) ) + | ~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from multiple.cpp:17: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::multcomp(std::vector&, std::string)': @@ -4340,6 +4410,11 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from plink.h:21, from merge.cpp:21: @@ -4347,6 +4422,11 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from haploTDT.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >' changed in GCC 7.1 @@ -4371,41 +4451,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5038 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from haploCC.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i&, int, bool)': -haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 48 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 62 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ -haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 79 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 93 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ -haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] - 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); - | ^ -haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': -haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 340 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 357 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ -haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 375 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 392 | if ( ! ( haploid || X && person->sex ) ) - | ~~^~~~~~~~~~~~~~ -g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-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 In file included from /usr/include/c++/10/vector:72, from haploCC.cpp:20: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -4425,17 +4471,27 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploTDT.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:67, + from haploTDT.cpp:20: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::haplotypicWeightedTDT()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from haploTDT.cpp:20: +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 In file included from poo.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 'unsigned int'} [-Wsign-compare] @@ -4458,29 +4514,9 @@ poo.cpp:328:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 328 | for (int c=0; c::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] 239 | double zt; | ^~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:67, - from haploTDT.cpp:20: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploPhase::haplotypicWeightedTDT()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from haploTDT.cpp:20: -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 In file included from helper.h:24, from webcheck.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -4503,20 +4539,6 @@ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 218 | for (int i=0; i::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from poo.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::perm_testTDT_POO(Perm&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -4553,7 +4575,31 @@ qfam.cpp:639:10: warning: unused variable 'tc' [-Wunused-variable] 639 | int tc = 0; | ^~ +In file included from /usr/include/c++/10/vector:72, + from poo.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from poo.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::perm_testTDT_POO(Perm&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from qfam.cpp:19: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 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 +/usr/include/c++/10/bits/vector.tcc: In member function 'void Plink::perm_testQTDT(Perm&)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -4564,22 +4610,16 @@ linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 50 | for (int i=0; i::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +linear.cpp: In member function 'double LinearModel::getPValue()': +linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] + 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; + | ^~~~ +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 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; @@ -4617,16 +4657,41 @@ bmerge.cpp:883:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 883 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:100:13: warning: 'irow' may be used uninitialized in this function [-Wmaybe-uninitialized] 100 | indxr[i]=irow; linear.cpp:108:7: warning: 'icol' may be used uninitialized in this function [-Wmaybe-uninitialized] 108 | if (ll != icol) { | ^~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void Plink::perm_testQTDT(Perm&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from mishap.cpp:20: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from linear.h:17, from linear.cpp:18: @@ -4641,6 +4706,17 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from bmerge.cpp:19: +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, + | ^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void LinearModel::fitLM()': /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); @@ -4655,6 +4731,11 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from linear.h:17, from linear.cpp:18: @@ -4666,34 +4747,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 -In file included from /usr/include/c++/10/algorithm:62, - from bmerge.cpp:19: -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2650 | __move_merge(_InputIterator __first1, _InputIterator __last1, - | ^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Locus*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:2650:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2717:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2717 | __merge_sort_with_buffer(_RandomAccessIterator __first, @@ -4746,24 +4799,6 @@ /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1318:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from mishap.cpp:20: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2488:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2488 | __merge_without_buffer(_BidirectionalIterator __first, @@ -5040,6 +5075,7 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +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 In file included from /usr/include/c++/10/bits/stl_algo.h:62, from /usr/include/c++/10/algorithm:62, from bmerge.cpp:19: @@ -5061,6 +5097,52 @@ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 1435 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from helper.h:24, + from legacy.cpp:22: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +legacy.cpp: In member function 'void Plink::calcRegression(int)': +legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 368 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 377 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 381 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 384 | for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 390 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 395 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 415 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 424 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 460 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] + 461 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] + 462 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 467 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] + 480 | for (int i=0; i >; _Distance = int; _Pointer = Locus*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:2427:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2427 | __merge_adaptive(_BidirectionalIterator __first, @@ -5153,53 +5235,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5038 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -In file included from helper.h:24, - from legacy.cpp:22: -options.h: In member function 'void OptionSet::display()': -options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -legacy.cpp: In member function 'void Plink::calcRegression(int)': -legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 368 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 377 | for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 381 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 384 | for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 390 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 395 | for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 415 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 424 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 460 | for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] - 461 | for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] - 462 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 467 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] - 480 | for (int i=0; i >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::calcRegression(int)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::calcRegression(int)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 673 | for (int i=0; i < plist.size(); i++) @@ -5287,6 +5321,7 @@ 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 segment.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -5365,51 +5400,6 @@ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ -In file included from /usr/include/c++/10/vector:72, - from homozyg.cpp:17: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from homozyg.cpp:17: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from segment.cpp:19: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from segment.cpp:19: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findSegments(int, int, vector_t&, std::ofstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findHomoRuns(Individual*, std::ofstream&)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from segment.cpp:19: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'vector_t Plink::perm_segmentIndividualTest(Perm&, bool, int, int, std::map&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void Plink::segmentIndividualTest(Perm&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 model.cpp:15: options.h: In member function 'void OptionSet::display()': @@ -5440,6 +5430,18 @@ 613 | double maxVIF = 0; | ^~~~~~ In file included from /usr/include/c++/10/vector:72, + from homozyg.cpp:17: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from homozyg.cpp:17: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, from model.h:17, from model.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -5456,14 +5458,31 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findHomoRuns(Individual*, std::ofstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from segment.cpp:19: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from segment.cpp:19: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::findSegments(int, int, vector_t&, std::ofstream&)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 '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 'unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from glm.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 294 | for (int h=1; h < whap->current->group.size(); h++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -glm.cpp:344:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 344 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 355 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] - 423 | for (int c=0; c::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'vector_t Plink::perm_segmentIndividualTest(Perm&, bool, int, int, std::map&)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void Plink::segmentIndividualTest(Perm&)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from logistic.h:17, from logistic.cpp:18: @@ -5515,13 +5525,7 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from linear.h:17, - from glm.cpp:17: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +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 dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] @@ -5559,24 +5563,31 @@ dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': -glm.cpp:610:28: warning: 'df' may be used uninitialized in this function [-Wmaybe-uninitialized] - 610 | double pvalue = chiprobP(chisq,df); - | ~~~~~~~~^~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from linear.h:17, - from glm.cpp:17: -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 elf.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 dfam.cpp +In file included from helper.h:24, + from glm.cpp:19: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from glm.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 294 | for (int h=1; h < whap->current->group.size(); h++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +glm.cpp:344:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 344 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 355 | for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] + 423 | for (int c=0; c >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from linear.h:17, + from glm.cpp:17: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +glm.cpp: In member function 'vector_t Plink::glmAssoc(bool, Perm&)': +glm.cpp:610:28: warning: 'df' may be used uninitialized in this function [-Wmaybe-uninitialized] + 610 | double pvalue = chiprobP(chisq,df); + | ~~~~~~~~^~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from linear.h:17, + from glm.cpp:17: +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 dfam.cpp +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from elf.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +elf.cpp: In member function 'bool RCount::addSNP(int)': +elf.cpp:374:10: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] + 374 | double wt; + | ^~ +In file included from /usr/include/c++/10/vector:72, + from plink.h:21, + from elf.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 +In file included from /usr/include/c++/10/vector:67, + from plink.h:21, + from elf.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] @@ -5650,18 +5717,6 @@ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 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 fisher.cpp -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from elf.cpp:18: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -elf.cpp: In member function 'bool RCount::addSNP(int)': -elf.cpp:374:10: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] - 374 | double wt; - | ^~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': @@ -5741,26 +5796,7 @@ fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from plink.h:21, - from elf.cpp:18: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from plink.h:21, - from elf.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 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); @@ -5781,7 +5817,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 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 'unsigned int'} [-Wsign-compare] @@ -5810,6 +5845,7 @@ 209 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -5886,6 +5920,8 @@ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ +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 +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 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 'unsigned int'} [-Wsign-compare] @@ -5896,10 +5932,6 @@ phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +pdriver.cpp: In member function 'void Plink::proxyWrapper()': +pdriver.cpp:266:11: warning: unused variable 'similar' [-Wunused-variable] + 266 | int similar = 0; + | ^~~~~~~ +In file included from haploQTL.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 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ +In file included from haploQTL.cpp:25: +phase.h: In member function 'void HaploPhase::reset()': +phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 252 | for (int i=0; i&, int, bool)': +haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 83 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 145 | for (int z = 0 ; z < hap1[i].size(); z++) + | ~~^~~~~~~~~~~~~~~~ +g++ -Wall -g -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 proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:939:58: warning: 'ref' may be used uninitialized in this function [-Wmaybe-uninitialized] 939 | haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " "; @@ -5926,31 +5980,11 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -In file included from haploQTL.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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ -In file included from haploQTL.cpp:25: -phase.h: In member function 'void HaploPhase::reset()': -phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] - 252 | for (int i=0; i&, int, bool)': -haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 83 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 145 | for (int z = 0 ; z < hap1[i].size(); z++) - | ~~^~~~~~~~~~~~~~~~ -g++ -Wall -g -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 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 '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 haplowindow.cpp In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6046,6 +6080,7 @@ haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wall -g -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 In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6109,30 +6144,7 @@ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from haplowindow.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploWindow::tallyUnambiguousCounts()': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from haplowindow.cpp:18: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from haplowindow.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploWindow::prunePhase(int, double)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 /usr/include/c++/10/vector:72, from haplohelper.cpp:19: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -6148,7 +6160,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 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 'unsigned int'} [-Wsign-compare] @@ -6168,8 +6179,31 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from haplowindow.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploWindow::tallyUnambiguousCounts()': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 clumpld.cpp +In file included from /usr/include/c++/10/vector:72, + from haplowindow.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from haplowindow.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void HaploWindow::prunePhase(int, double)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from nonfounderphasing.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 'unsigned int'} [-Wsign-compare] @@ -6184,6 +6218,7 @@ genogroup.h:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6207,6 +6242,7 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +g++ -Wall -g -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 In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6262,21 +6298,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 -In file included from /usr/include/c++/10/algorithm:62, - from clumpld.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from clumpld.cpp:18: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ResultTrio; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ 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 'unsigned int'} [-Wsign-compare] @@ -6321,66 +6342,13 @@ genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 358 | for (int z2=0; z2::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ResultTrio&}; _Tp = ResultTrio; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from clumpld.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1662 | __heap_select(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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 /usr/include/c++/10/vector:72, from genoerr.cpp:19: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1937 | std::__heap_select(__first, __middle, __last, __comp); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from clumpld.h:17, - from clumpld.cpp:20: -/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector clump_LD::read_assoc_file(std::string)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from clumpld.cpp:18: -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 em.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 'unsigned int'} [-Wsign-compare] @@ -6422,7 +6390,53 @@ em.cpp:166:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 166 | for (int z=0; z >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from clumpld.cpp:18: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ResultTrio; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from clumpld.h:17, + from clumpld.cpp:20: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ResultTrio&}; _Tp = ResultTrio; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ 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 impute.cpp +In file included from /usr/include/c++/10/algorithm:62, + from clumpld.cpp:18: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1662 | __heap_select(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1937 | std::__heap_select(__first, __middle, __last, __comp); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 metaem.cpp In file included from impute.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 'unsigned int'} [-Wsign-compare] @@ -6463,7 +6477,28 @@ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ -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 metaem.cpp +In file included from /usr/include/c++/10/vector:67, + from clumpld.h:17, + from clumpld.cpp:20: +/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector clump_LD::read_assoc_file(std::string)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from clumpld.cpp:18: +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -6533,12 +6568,6 @@ 667 | for (int l=0; l::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double2&}; _Tp = double2; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from nlist.h:21, from nlist.cpp:17: @@ -6546,10 +6575,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 38 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from profile.cpp:19: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double2&}; _Tp = double2; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from profile.cpp:19: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::scoreIndividuals()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 +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 simul.cpp In file included from helper.h:24, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -6628,6 +6660,10 @@ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::scoreIndividuals()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ @@ -6685,7 +6721,6 @@ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ -g++ -Wall -g -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 simul.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': @@ -6714,13 +6749,6 @@ 1358 | double cumA = 0, cumU = 0; | ^~~~ In file included from /usr/include/c++/10/vector:72, - from whap.h:18, - from whap.cpp:19: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, from plink.h:21, from simul.cpp:15: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SimParameters&}; _Tp = SimParameters; _Alloc = std::allocator]': @@ -6731,6 +6759,13 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SimParametersQT&}; _Tp = SimParametersQT; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:72, + from whap.h:18, + from whap.cpp:19: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from plink.h:21, from simul.cpp:15: @@ -6744,23 +6779,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::simulateSNPs_QT()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 In file included from helper.h:24, from gvar.cpp:15: @@ -6768,7 +6786,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -g++ -Wall -g -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 gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 125 | for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 556 | for (int i=0; i >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::simulateSNPs_QT()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 +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 step.cpp In file included from helper.h:24, from cnv.cpp:23: options.h: In member function 'void OptionSet::display()': @@ -6896,35 +6932,12 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from cnv.cpp:18: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -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 step.cpp In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from cnv.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readCNVList()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 greport.cpp In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -6954,12 +6967,22 @@ 125 | int cnt = 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 flip.cpp +In file included from /usr/include/c++/10/vector:72, + from cnv.cpp:18: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ 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 qualscores.cpp In file included from helper.h:24, from qualscores.cpp:24: @@ -6971,37 +6994,37 @@ qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ +In file included from /usr/include/c++/10/vector:67, + from cnv.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::readCNVList()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: 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 '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 cfamily.cpp +In file included from cfamily.cpp:18: +options.h: In member function 'void OptionSet::display()': +options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] + 73 | for ( int k = 0 ; k < i->second.size(); k++) + | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from cnvqt.cpp:18: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from cnvqt.cpp:18: -/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Plink::testCNVwithQT(double, int, int, vector_t&, vector_t&, vector_t&)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 'unsigned int'} [-Wsign-compare] - 73 | for ( int k = 0 ; k < i->second.size(); k++) - | ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) @@ -7022,7 +7045,20 @@ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from cnvqt.cpp:18: +/usr/include/c++/10/bits/stl_vector.h: In member function 'vector_t Plink::testCNVwithQT(double, int, int, vector_t&, vector_t&, vector_t&)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 'unsigned int'} [-Wsign-compare] @@ -7041,29 +7077,6 @@ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ -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 -In file included from /usr/include/c++/10/bits/stl_algo.h:61, - from /usr/include/c++/10/algorithm:62, - from setscreen.cpp:18: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SortedResult; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from setscreen.cpp:18: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7074,13 +7087,6 @@ options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from options.h:18, - from setscreen.cpp:21: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SortedResult&}; _Tp = SortedResult; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) @@ -7115,28 +7121,6 @@ idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from options.h:18, - from setscreen.cpp:21: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::setAssocSummary()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from setscreen.cpp:18: -/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1974 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1975 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1976 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1891 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 502 | if ( ++p == tokens.size() ) @@ -7243,6 +7227,13 @@ idhelp.cpp:1085:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/bits/stl_algo.h:61, + from /usr/include/c++/10/algorithm:62, + from setscreen.cpp:18: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SortedResult; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ @@ -7320,6 +7311,13 @@ idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from setscreen.cpp:18: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 idhelp.cpp:1903:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 1903 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ @@ -7368,14 +7374,43 @@ idhelp.cpp:2234:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from options.h:18, + from setscreen.cpp:21: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SortedResult&}; _Tp = SortedResult; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from options.h:18, + from setscreen.cpp:21: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::setAssocSummary()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from setscreen.cpp:18: +/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1974 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1975 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1976 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1891 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 '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 hapglm.cpp In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': @@ -7409,6 +7444,7 @@ 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 +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 lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': @@ -7428,7 +7464,6 @@ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ -g++ -Wall -g -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 blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7505,7 +7540,6 @@ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 513 | for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 548 | for (int f = 0 ; f < vzin.size() ; f++ ) | ~~^~~~~~~~~~~~~ @@ -7535,6 +7569,7 @@ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] 190 | int geno_field = a2_field + skip2 + 1; | ^~~~~~~~~~ +g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] @@ -7630,6 +7665,12 @@ metaanal.cpp:680:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 680 | for (int f=0; f::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from stats.h:19, - from metaanal.cpp:20: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::metaAnalysis()': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 r.cpp -In file included from Rconnection.h:42, - from r.cpp:29: -Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] - 327 | #warning using little endian based on information from endian.h - | ^~~~~~~ In file included from helper.h:24, from r.cpp:19: options.h: In member function 'void OptionSet::display()': @@ -7683,6 +7708,31 @@ r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ +In file included from /usr/include/c++/10/vector:67, + from stats.h:19, + from metaanal.cpp:20: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void Plink::metaAnalysis()': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] + 380 | delete rCov; + | ^~~~ +r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] + 378 | delete rS; + | ^~ +r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] + 377 | delete rP; + | ^~ +r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] + 376 | delete rN; + | ^~ +r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] + 399 | delete rc; + | ^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.h:42, from Rconnection.cpp:30: @@ -7720,21 +7770,6 @@ 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; | ^~~~ -r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] - 380 | delete rCov; - | ^~~~ -r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] - 378 | delete rS; - | ^~ -r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] - 377 | delete rP; - | ^~ -r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] - 376 | delete rN; - | ^~ -r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] - 399 | delete rc; - | ^~ g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp g++ -Wall -g -fdebug-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/plink-1.07+dfsg' @@ -7774,8 +7809,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-3_armhf.deb'. dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-3_armhf.deb'. +dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-3_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../plink_1.07+dfsg-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -7783,12 +7818,14 @@ 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/23815/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/23815/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/24315 and its subdirectories -I: Current time: Mon Sep 6 13:56:42 -12 2021 -I: pbuilder-time-stamp: 1630979802 +I: removing directory /srv/workspace/pbuilder/23815 and its subdirectories +I: Current time: Tue Sep 7 16:14:19 +14 2021 +I: pbuilder-time-stamp: 1630980859