I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 15 11:18:28 -12 2020 I: pbuilder-time-stamp: 1602803908 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [plink_1.07+dfsg-2.dsc] I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Sep 18 18:15:45 2018 -12 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "bob.dybian@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plink_1.07+dfsg-2.dsc dpkg-source: info: extracting plink in plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23344/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 parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='90314b4e54e945b28b58a3ec2a918c17' 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='23344' PS1='# ' PS2='> ' 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.NEvuCV0ius/pbuilderrc_3kyr --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.NEvuCV0ius/b1 --logfile b1/build.log plink_1.07+dfsg-2.dsc' SUDO_GID='114' SUDO_UID='109' 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/' I: uname -a Linux jtx1a 4.19.0-11-arm64 #1 SMP Debian 4.19.146-1 (2020-09-17) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 6 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/23344/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 18.4 MB of archives. After unpacking 63.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Fetched 18.4 MB in 2s (9635 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../22-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../27-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../33-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_clean make -j3 clean make[2]: Entering directory '/build/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-1.07+dfsg' /usr/bin/make CXXFLAGS='-Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make[2]: Entering directory '/build/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp In file included from plink.cpp:28: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from plink.cpp:35: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp In file included from input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i == include.size() ) ~~^~~~~~~~~~~~~~~~~ input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_clst) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:821:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i=2; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] else if ( ccount != tokens.size() ) ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_pheno) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_covar) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1261:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::clist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1519:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::plist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::__cxx11::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from plink.h:21, from input.cpp:23: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from input.cpp:23: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readSegmentFile(std::ifstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readSegmentFileMinimal(std::ifstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readHomozygSegmentFile(std::ifstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from input.cpp:23: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from input.cpp:23: /usr/include/c++/8/bits/stl_vector.h: In member function 'bool Plink::readCovListFile()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'bool Plink::readMultiplePhenoFile()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:62, from /usr/include/c++/8/algorithm:62, from input.cpp:18: /usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Temporary_buffer<_ForwardIterator, _Tp>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from input.cpp:18: /usr/include/c++/8/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++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from input.cpp:23: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readMapFile(std::__cxx11::string, std::vector&, std::vector&, int&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from input.cpp:18: /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:91:13: warning: 'PED' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( feof(PED) ) ~~~~^~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp 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] 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] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] while (c<7 && s::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from binput.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from binput.cpp:22: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:62, from /usr/include/c++/8/algorithm:62, from binput.cpp:19: /usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Temporary_buffer<_ForwardIterator, _Tp>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from binput.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from binput.cpp:22: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readBinData()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from binput.cpp:19: /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp In file included from tinput.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( c > sample.size()) ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( gn != 2 * sample.size() ) ~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from tinput.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from tinput.cpp:23: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:62, from /usr/include/c++/8/algorithm:62, from tinput.cpp:19: /usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Temporary_buffer<_ForwardIterator, _Tp>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from tinput.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from tinput.cpp:23: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readTransposedData()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from tinput.cpp:19: /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp In file included from genome.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^~~~~~~ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^~~~~~ genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^~ genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^~~ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^~~ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^~~ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~^~~~~~~~ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::__cxx11::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int t=0; t > CArgs::value(std::__cxx11::string, int)': helper.cpp:267:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( (i+j) < a.size() ) ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (r.size() != c) error("Not enough arguments given for option: "+s+" "); ~~~~~~~~~^~~~ helper.cpp: In function 'std::vector > parse2str(std::__cxx11::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0 ; i < s.length() ; i++) ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] if (s[i] == ',' || i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ helper.cpp:309:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] if (i == s.length()-1) t += s[i]; ~~^~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector parse2int(std::__cxx11::string)': helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while(h >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s = 0 ; s < snps.size() ; s++) ~~^~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string chromosomeName(int)': helper.cpp:952:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( c < 0 || c >= par::chr_code.size() ) ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'int getMarkerChromosome(Plink&, std::__cxx11::string)': helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i getChromosomeRange(Plink&)': helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->fid.length() > par::pp_maxfid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->iid.length() > par::pp_maxiid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (locus[l]->name.length() > par::pp_maxsnp) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=1; j, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&)': helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( input.size() != P.nl_all ) ~~~~~~~~~~~~~^~~~~~~~~~~ helper.cpp: In function 'std::map, std::set > readRange(std::__cxx11::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^~~~ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^~~~~~~~~~~~~~ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^~~~~~~~~~~~~~ helper.cpp: In member function 'std::__cxx11::string CArgs::value(std::__cxx11::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'int CArgs::value_int(std::__cxx11::string)': helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::__cxx11::string)': helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'double CArgs::value_double(std::__cxx11::string)': helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'int getInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:378:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:391:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'double getDouble(std::__cxx11::string, std::__cxx11::string)': helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid numeric argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/8/vector:69, from helper.h:18, from helper.cpp:24: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wmaybe-uninitialized] cur[maxI] = false; ^ In file included from /usr/include/c++/8/vector:64, from helper.h:18, from helper.cpp:24: /usr/include/c++/8/bits/stl_vector.h: In function 'void sizeMatrix(matrix_t&, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^~~ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^~~ stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < v.size(); i++) ~~^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from stats.h:19, from stats.cpp:24: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from stats.h:19, from stats.cpp:24: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector > msqrt(std::vector >&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector > svd_inverse(std::vector >&, bool&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'Eigen eigenvectors(std::vector >&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int l = 0 ; l < locus.size() ; l++ ) ~~^~~~~~~~~~~~~~ filters.cpp:762:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < sample.size() ; i++ ) ~~^~~~~~~~~~~~~~~ filters.cpp:1078:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void Plink::preCalcSinglePoint()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from options.h:18, from multi.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::preCalcMultiPoint()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from options.h:18, from multi.cpp:16: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from helper.h:24, from cluster.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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=1; z<=qt.size(); z++) ~^~~~~~~~~~~ cluster.cpp:452:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0;k >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=i+1; j::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cluster.cpp:1038:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int j=0;j >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; ~~~~~~~~~^~~~~ cluster.cpp:1049:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j1=0; j1 >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j2=0; j2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >; _Distance = int; _Tp = Neighbour; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from cluster.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from cluster.cpp:22: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from cluster.cpp:22: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::groupGenome()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::buildCluster()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from cluster.cpp:19: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from cluster.cpp:22: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from mds.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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i1=0; i1::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i2=0; i2::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( elist.size() != par::cluster_mds_dim ) ~~~~~~~~~~~~~^~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp In file included from output.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::iterator loc1 = locus.begin()+m1; ^~~~ output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] vector::iterator loc2 = locus.begin()+m2; ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < setname.size();i++) ~~^~~~~~~~~~~~~~~~ output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Z&}; _Tp = Z; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from informative.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'int Plink::calcInformative()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'int Plink::readInformative()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp 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] 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] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^~~~ assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1109:61: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); ~~~~~^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from assoc.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from assoc.cpp:21: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::calcAssociationWithPermutation(Perm&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int e=0;e >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] if (len != tokens.size() - offset ) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ prephap.cpp:283:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = allele ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ prephap.cpp:412:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] while ( index < tokens.size() ) ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:34: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens[index].size() != len ) ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( index == tokens.size() - 1 ) ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&)': phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z, int>::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( nh != hapmap.size() ) ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < pp[i].size() ; z++ ) ~~^~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < h1.size(); z++) ~~^~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from phase.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from phase.cpp:19: /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::enumerateHaplotypes(std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::prunePhase(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::performAlternEM()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:272:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:335:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp:350:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0;f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; kpm->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; kpp->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; iperson.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c < fam->kid.size(); c++) ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from tdt.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::perm_testTDT(Perm&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp In file included from perm.h:17, from sharing.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ genepi.cpp: In function 'long double pillai(int, int, int, double)': genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] bool casewise_deletion = false; ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from genepi.cpp:19: /usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from genepi.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from plink.h:21, from genepi.cpp:23: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from genepi.cpp:23: /usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from genepi.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void CCA_caseonly(bool, std::vector >&, Set&, Plink&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __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] gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; ^ In file included from /usr/include/c++/8/algorithm:62, from genepi.cpp:19: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int s=0;s >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] else if (par::set_min > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if (par::set_max==-1 || par::set_max > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=j+1; k < snpset[i].size(); k++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >; _Distance = int; _Tp = SetSortedSNP; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from sets.cpp:16: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from sets.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from sets.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Set::profileTestSNPInformation(int, double)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'vector_t Set::profileTestScore()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from sets.cpp:16: /usr/include/c++/8/bits/stl_algo.h: In member function 'vector_t Set::fitLDSetTest(vector_t&, bool)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i=0; i&, std::vector&)': perm.cpp:273:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j< P.pS->snpset[l].size();j++) ~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from perm.cpp:15: /usr/include/c++/8/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_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from perm.cpp:15: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from perm.cpp:15: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Pair2; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from perm.cpp:15: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'bool Perm::update(std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from options.h:18, from perm.h:17, from perm.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Pair2&}; _Tp = Pair2; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from options.h:18, from perm.h:17, from perm.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Perm::setOriginalRanking(vector_t&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from perm.cpp:15: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; kkids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::__cxx11::string, std::__cxx11::string, bool, bool, std::ofstream&, std::map, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] if (write) ^~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from merge.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:62, from /usr/include/c++/8/algorithm:62, from merge.cpp:19: /usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Temporary_buffer<_ForwardIterator, _Tp>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from merge.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from merge.cpp:21: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::mergeData()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from merge.cpp:19: /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp In file included from hotel.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (!sample[i]->missing) ^ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from hotel.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In function 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void calcHotelSetMeanVariance(std::vector&, std::vector&, std::vector&, std::vector >&, std::vector&, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::__cxx11::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >; _Distance = int; _Tp = Pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from multiple.cpp:18: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from multiple.cpp:17: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from multiple.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::multcomp(std::vector&, std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from multiple.cpp:18: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp In file included from haploCC.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); ^ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from haploCC.cpp:20: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from haploCC.cpp:20: /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::haplotypicWeightedCC()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from haploCC.cpp:20: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from haploTDT.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void HaploPhase::haplotypicWeightedTDT()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from poo.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::perm_testTDT_POO(Perm&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp In file included from helper.h:24, from webcheck.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( i < tokens.size() - 1) ~~^~~~~~~~~~~~~~~~~~~ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < family.size(); i++) ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0 ; f < family.size() ; f++) ~~^~~~~~~~~~~~~~~ qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < (*f)->kid.size() ; k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void Plink::perm_testQTDT(Perm&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp In file included from helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from linear.h:17, from linear.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LinearModel::displayResults(std::ofstream&, Locus*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LinearModel::fitLM()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from linear.h:17, from linear.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from linear.h:17, from linear.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LinearModel::pruneY()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LinearModel::setDependent()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] long int inc; ^~~ bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~~~ bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from bmerge.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:62, from /usr/include/c++/8/algorithm:62, from bmerge.cpp:19: /usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Locus]': /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Temporary_buffer<_ForwardIterator, _Tp>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from bmerge.cpp:19: /usr/include/c++/8/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++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from bmerge.cpp:21: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::mergeBinaryData()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from bmerge.cpp:19: /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _TmpBuf __buf(__first, __last); ^~~~~ /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp In file included from 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without void setOptions(CArgs & a) ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp In file included from mishap.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Segment&}; _Tp = Segment; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': legacy.cpp:203:18: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized] << start - last - 1 << " "; ~~~~~~^~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from legacy.cpp:21: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from legacy.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from legacy.cpp:21: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::preCalcRegression_PIHAT()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::calcRegression(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:861:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1178:31: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< (*pA)->segs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:33: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( (*pA)->match[i].size() >= maxlist ) ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] homozygWindows[l] == 0; In file included from /usr/include/c++/8/vector:69, from homozyg.cpp:17: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from homozyg.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::findHomoRuns(Individual*, std::ofstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::__cxx11::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!ibd) ^~ segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' SIBS << setw(10) << original[l] << " " ^~~~ segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0;ifirst; ^ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] int nseg = smap.size(); ^~~~ segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from segment.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from segment.cpp:19: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::findSegments(int, int, vector_t&, std::ofstream&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from segment.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'vector_t Plink::perm_segmentIndividualTest(Perm&, bool, int, int, std::map&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'vector_t Plink::perm_segmentIndividualTest(Perm&, bool, int, int, std::map&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp In file included from model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from model.cpp:17: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&)': model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( include.size() != P->n ) ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< par::parameter_list.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < X.size() ; i++) ~~^~~~~~~~~~ model.cpp:374:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < par::parameter_list.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] double maxVIF = 0; ^~~~~~ model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] error("Internal problem with QFAM model specification"); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from model.h:17, from model.cpp:14: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from model.h:17, from model.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'double Model::linearHypothesis(matrix_t&, vector_t&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp In file included from helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from logistic.h:17, from logistic.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LogisticModel::displayResults(std::ofstream&, Locus*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void LogisticModel::HuberWhite()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp 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] 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] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=1; h < whap->current->group.size(); h++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c::_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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 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] double pvalue = chiprobP(chisq,df); ~~~~~~~~^~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from linear.h:17, from glm.cpp:17: /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c 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] if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~~~~~^~~~~~~~~~~~~ dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; ^~~ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp In file included from helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l< original.size(); l++) ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] const double pthresh = 0.01; ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] bool one_sided = true; ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] int srange_cnt = 0; ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] bool inRange = false; ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++) ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != ncol ) ~~~~~~~~~~~~~~^~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from elf.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:374:10: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] double wt; ^~ elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1154:8: warning: 'p_gcnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_gcnt); ^~~~~~~~~~~ elf.cpp:1165:5: warning: 'p_cnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_cnt); ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from elf.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from plink.h:21, from elf.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from plink.h:21, from elf.cpp:18: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void Plink::permTestRareDistribution(Perm&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:106:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] bool informative = false; ^~~~~~~~~~~ dfam.cpp:504:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] int totalInformative = 0; ^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:449:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (*ncol <= 1) ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' for (i = 1; i <= *ldkey << 1; ++i) { ^~~ fisher.cpp:501:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(20, "This should never occur."); ^ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:164:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::__cxx11::string, int, std::__cxx11::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] char out_buf[BUF_SIZE+1]; // Output buffer for GET request ^~~~~~~ sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] char in_buf[BUF_SIZE+1]; // Input buffer for response ^~~~~~ sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] unsigned int i; // Loop counter ^ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] int echoStringLen = 100; ^~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( added.size() >= par::proxy_snp_filter ) ~~~~~~~~~~~~~^~~~~~ proxy.cpp:854:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c1 = 0; c1 < collection.size() ; c1++ ) ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] int t1=0; ^~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] CSNP * s = SNP[l]; ^ In file included from /usr/include/c++/8/vector:69, from options.h:18, from proxy.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:939:58: warning: 'ref' may be used uninitialized in this function [-Wmaybe-uninitialized] haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " "; ^ In file included from /usr/include/c++/8/vector:64, from options.h:18, from proxy.cpp:21: /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp In file included from pdriver.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploQTL.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l < actual_map.size(); l++) ~~^~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] ||alleles2.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[p1].size(); z++) ~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z1 = 0; z1 < hap1[p1].size(); z1++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z2 = 0; z2 < hap1[p2].size(); z2++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] int j=0; ^ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < windows[w]->hap1[r].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from haplohelper.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from haplohelper.cpp:19: /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::enumerateAllPhases()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (h::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from haplowindow.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploWindow::tallyUnambiguousCounts()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z < pp[i].size(); z++) ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] int pcnt=1; ^~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] double posterior = ip->second; ^~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from nonfounderphasing.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from nonfounderphasing.cpp:19: /usr/include/c++/8/bits/stl_vector.h: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i clump_LD::read_assoc_file(std::__cxx11::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int f=0; f >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( f < annot_field.size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < sp.size(); i++) ~~^~~~~~~~~~~ clumpld.cpp:480:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if( l1 < P->locus.size()-1 ) ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] if( j < grouped_snps.size()-1) ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from clumpld.cpp:18: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from clumpld.cpp:18: /usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from clumpld.cpp:18: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from clumpld.h:17, from clumpld.cpp:20: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from clumpld.h:17, from clumpld.cpp:20: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector clump_LD::read_assoc_file(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from clumpld.cpp:18: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from clumpld.h:18, from clumpld.cpp:20: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = ClumpPair; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from clumpld.h:18, from clumpld.cpp:20: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = ClumpPair; _Tp = ClumpResults; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for( int a = 0; a < posshap1.size(); a++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for( int b = 0; b < posshap2.size(); b++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z2=0; z2::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void HaploPhase::queryThisGenotype(int, int, int, vector_t&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c 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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->hap1[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->pp[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s < g.size(); s++) ~~^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] bool OLD_clist = par::clist; ^~~~~~~~~ profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( qcnt == qlabel.size() ) ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] bool a1 = i2->second; ^~ profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] bool sawNamedAllele = false; ^~~~~~~~~~~~~~ profile.cpp:629:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from profile.cpp:19: /usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::scoreIndividuals()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp In file included from helper.h:24, from nlist.h:21, from nlist.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::__cxx11::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i NList::deparseStringList(std::__cxx11::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i > NList::tokenize(std::__cxx11::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( s[i]== range_char && i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] else if ( i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp In file included from helper.h:24, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int g = 0; g < nullModel.group.size(); g++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int g=0; g::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g=0; g >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g2=0; g2 >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( g < nullModel.group.size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s < conditioner.size(); s++) ~~^~~~~~~~~~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< tok.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < tok.size() ; i++ ) ~~^~~~~~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( mapping.size() != H->ns + H->nh ) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i< lst.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1142:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int g=0; g< model.group.size(); g++) ~^~~~~~~~~~~~~~~~~~~~ whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c=0; c < P->conditioner.size(); c++) ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l&, ChapModel&)': whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0;l >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int h=0; h < m.group.size(); h++) ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( cnt>0 && cnt2 < m.group[h].size() ) ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from whap.h:18, from whap.cpp:19: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'vector_t Plink::conditionalHaplotypeTest(bool, Perm&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] double gh_11_12 = h11*h12; ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SimParameters&}; _Tp = SimParameters; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from plink.h:21, from simul.cpp:15: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::simulateSNPs()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::simulateSNPs_QT()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24, from gvar.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~ gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] bool fatal = false; ^~~~~ gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'Model* analyseModel(Plink*, Variant*, int, bool, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'Model* analyseModel(Plink*, Variant*, int, bool, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp In file included from helper.h:24, from cnv.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] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:678:36: warning: variable 'is' set but not used [-Wunused-but-set-variable] map::iterator is = idescription.find(*ir); ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s1=0; s1::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s2=s1+1; s2::iterator i2 = isection.begin(); ^~ cnv.cpp:1103:36: warning: variable 'il' set but not used [-Wunused-but-set-variable] map::iterator il = segmentLength.find(t); ^~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] int nseg = 1; ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] int nseg=0; ^~~~ cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int c = 0 ; c < scaffold.size(); c++) ~~^~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] noCovar == true; ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] indivPair p = ic->first; ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ In file included from /usr/include/c++/8/vector:69, from cnv.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = Segment; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from cnv.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::readCNVList()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:19: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int l=0; l< ari->second.size(); l+=2) ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] long int nfound = 0; ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from cnvqt.cpp:18: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from cnvqt.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In member function 'vector_t Plink::testCNVwithQT(double, int, int, vector_t&, vector_t&, vector_t&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:221:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != cols ) ~~~~~~~~~~~~~~^~~~~~~ setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < pS->snpset.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i < snpset[j].size(); i++) ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from setscreen.cpp:18: /usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from setscreen.cpp:18: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from options.h:18, from setscreen.cpp:21: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from options.h:18, from setscreen.cpp:21: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::setAssocSummary()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from setscreen.cpp:18: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::__cxx11::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:63:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int g=0; gvalues.size(); g++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::map >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( found != matchTemplate.size() ) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] bool match = true; ^~~~~ idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < mask.size() ; i++) ~~^~~~~~~~~~~~~ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] vector & jo = jointOrder[j]; ^~ idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( p < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:547:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:553:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] bool seenJoint = true; ^~~~~~~~~ idhelp.cpp:584:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:594:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:678:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:747:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] set & jf = jointField[j]; ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != file->uniqFieldCount ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( j < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i=0; i::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( v->value.size() + 3 > myField->width ) ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] IDGroup * group = idgroup[g]; ^~~~~ idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0; k < (*i0)->values.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; zvalues.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int z=0; z<(*i0)->values.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0 ; f < targetFields.size(); f++) ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size(); i++) ~~^~~~~~~~~~~~~~~ idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= maxfield ) ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < thisGroup->values.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int s=0; s< par::idhelp_match_string.size(); s+=2) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0 ; f < fieldNames.size(); f++) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:22: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( maxF >= tok.size() ) ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int v=0; vvalues.size(); v++) ~^~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] bool jointQuery = id.find("+") != string::npos; ^~~~~~~~~~ idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k = 0 ; k < thisLine.size() ; k++ ) ~~^~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from whap.h:18, from hapglm.cpp:19: /usr/include/c++/8/bits/stl_vector.h: In member function 'vector_t Plink::glmHaplotypeTest(bool, Perm&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from helper.h:24, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int t = 0 ; t < tokens.size() ; t++) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] int nsnps = toPosition - fromPosition + 1; ^~~~~ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] int numStrong = 0; ^~~~~~~~~ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] int numRec = 0; ^~~~~~ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] int numInGroup = 0; ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int k=0; k0 ) loglike1 += knownBA * log( pB1 ); ~~~^~~~~~~ blox.cpp:505:10: warning: 'pB1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ blox.cpp:503:10: warning: 'pA2' may be used uninitialized in this function [-Wmaybe-uninitialized] double pA = pA1 + pA2; ^~ blox.cpp:505:10: warning: 'pA1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp In file included from helper.h:24, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int q = 0 ; q < qthresh.size() ; q++) ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0 ; f < vzin.size() ; f++ ) ~~^~~~~~~~~~~~~ dosage.cpp:581:20: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tok.size() < firstCol ) ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=firstCol; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < personMap[f].size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:24: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != expected[f] ) dosage.cpp:989:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int q=0; qgetStatistic() : 0; ^~~~~~~~~ dosage.cpp:1252:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( o->second != dosageFilename_all.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if ( ++qq == qthresh.size() ) ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] int geno_field = a2_field + skip2 + 1; ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from options.h:18, from dosage.cpp:20: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from options.h:18, from dosage.cpp:20: /usr/include/c++/8/bits/stl_vector.h: In function 'void setUpQScoring(std::map, double>&, std::vector&, std::vector >&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ dosage.cpp: In member function 'void Plink::processDosageFile()': dosage.cpp:915:21: warning: 'snp_code' may be used uninitialized in this function [-Wmaybe-uninitialized] SNP[snp_code]->one[personPosition[f][i]] = s1; ^ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:9: warning: unused variable 'include' [-Wunused-variable] bool include = false; ^~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor 'Alleles::Alleles(std::__cxx11::string, int, int, std::__cxx11::string, std::__cxx11::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] int bp; ^~ metaanal.cpp:44:10: warning: 'std::__cxx11::string Alleles::a1' [-Wreorder] string a1; ^~ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] Alleles(string name, int chr, int bp, string a1, string a2) ^~~~~~~ metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f = 0 ; f < par::meta_files.size() ; f++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != fsize ) ~~~~~~~~~~~~~~^~~~~~~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] int pval_column = -1; ^~~~~~~~~~~ metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int f=0; f::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from stats.h:19, from metaanal.cpp:20: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Plink::metaAnalysis()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from Rconnection.h:42, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] #warning using little endian based on information from endian.h ^~~~~~~ In file included from helper.h:24, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] int ct = data->length(); ^~ r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rCov; ^~~~ r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rS; ^~ r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rP; ^~ r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rN; ^~ r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rc; ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.h:42, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] #warning using little endian based on information from endian.h ^~~~~~~ In file included from Rconnection.cpp:30: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (host) free(host); host=0; ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (host) free(host); host=0; ^~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/plink-1.07+dfsg' make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/plink/usr/lib/debian-med/bin/plink contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/plink/usr/lib/debian-med/bin/plink was not linked against libdl.so.2 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-2_armhf.deb'. dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../plink_1.07+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: 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/23344 and its subdirectories I: Current time: Thu Oct 15 12:22:02 -12 2020 I: pbuilder-time-stamp: 1602807722