Sat May 6 02:34:46 UTC 2023 I: starting to build plink/bookworm/arm64 on jenkins on '2023-05-06 02:34' Sat May 6 02:34:46 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/28944/console.log Sat May 6 02:34:46 UTC 2023 I: Downloading source for bookworm/plink=1.07+dfsg-4 --2023-05-06 02:34:46-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/plink/plink_1.07%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2076 (2.0K) [text/prs.lines.tag] Saving to: ‘plink_1.07+dfsg-4.dsc’ 0K .. 100% 135M=0s 2023-05-06 02:34:46 (135 MB/s) - ‘plink_1.07+dfsg-4.dsc’ saved [2076/2076] Sat May 6 02:34:46 UTC 2023 I: plink_1.07+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: plink Binary: plink Architecture: any Version: 1.07+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy , Dylan Aïssi Homepage: http://zzz.bwh.harvard.edu/plink/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/plink Vcs-Git: https://salsa.debian.org/med-team/plink.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev Package-List: plink deb science optional arch=any Checksums-Sha1: c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz 30da84e59157c428d54473d7e242e394a2dc6aaf 17356 plink_1.07+dfsg-4.debian.tar.xz Checksums-Sha256: e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz 9cf0a2845eb96c95ed85347bdaf8afcc7bb0c933c960ce2adde2026ec78084c4 17356 plink_1.07+dfsg-4.debian.tar.xz Files: fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz d4701d1cd62de5c466ad92f54f17c8c8 17356 plink_1.07+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmF+uA0SHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxETcP/3wRcCdwV0xLxdFXTmzylhrUKT5kjY0U Pk29v5hnbrVOL3Bi07N+m3OELa/CTv3WbwaOaz40x5nGp0lIggSMnuXEwMu0Hor9 OLj5ikYYfZiOPoK0/UoS5FVg6MHTtboRzaCi30WEtf1BP+c8LlMz0xjX9alG5kHR VnyNRSbpCDQ0ZNk/GQyV9UO4z2HlAelHe8scw38ftO30kW2wgfCf1faiwL2UTbmb iST+7qZKGz3Us0QhSo9JcC9TNweeRC7qLY/bmKZZ9/EoNPDXQMed5fa21Vt+gCRo U/s68xdFb6X2hVGEZHSLDnILvUDKbWBNvHtIPvfxfbR3214wldyrpslBvVUxYEB1 /8OuUEJjy5Q1L9jaqtxtIvWQ2j4XXEWp63f65P8HaTr6Ep73w6zPu9datP18OjA9 YxhZm28w5gWFInWIAm1l196WyYyVvD5/4ne9H+rJxbcWYx/TVnhd9CB1YxDrRxLV xO93tEzYwuMRE5OvjCAWlkfXdLuLz1dQHGUxZxKMTpuRKi1ZK+c5nJPlFko0KCl+ 33AEuGa+78KCVNltyZz11xRclvXGmdtmvLaSaPf9HuRf+oQInt0F08GoEXc6W/RN f+bVMGjwp6nKc8C++GIkafYVhk79PVelGhCUFo18QZEiPMplNKaAVS2TaBzcL1qo 3MfYJHMkPP1/ =yj3Z -----END PGP SIGNATURE----- Sat May 6 02:34:46 UTC 2023 I: Checking whether the package is not for us Sat May 6 02:34:46 UTC 2023 I: Starting 1st build on remote node codethink10-arm64.debian.net. Sat May 6 02:34:46 UTC 2023 I: Preparing to do remote build '1' on codethink10-arm64.debian.net. Sat May 6 02:48:00 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 5 14:34:49 -12 2023 I: pbuilder-time-stamp: 1683340489 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [plink_1.07+dfsg-4.dsc] I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Oct 31 03:36:45 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting plink in plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29555/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='29555' 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/r-b-build.VTBpSLxw/pbuilderrc_7zMn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink10-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 4 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29555/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 75.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Fetched 19.3 MB in 0s (47.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../plink_1.07+dfsg-4_source.changes dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_clean make -j8 clean make[2]: Entering directory '/build/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make -j8 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1 make[2]: Entering directory '/build/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp 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 input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 516 | if ( i == include.size() ) | ~~^~~~~~~~~~~~~~~~~ input.cpp:521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 521 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ input.cpp:545:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 545 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 579 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 695 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from helper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::readClusterFile(bool)': input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 787 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp:817:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 821 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] 897 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 927 | for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 961 | else if ( ccount != tokens.size() ) | ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1037 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1043 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1064 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1208 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1232 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1256 | if (tokens.size() < 2+par::mult_covar) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ input.cpp:1261:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1261 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1335 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 58 | for (int i=0; i >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 79 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 90 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 100 | for (int i=0; i< m.size(); i++) | ~^~~~~~~~~~ input.cpp:1519:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1538 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1572 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1599 | else if (tokens.size() != par::plist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1602 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1792 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2225 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2471 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 193 | for (int t=0; t >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > CArgs::value(std::string, int)': helper.cpp:267:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 267 | if ( (i+j) < a.size() ) | ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); | ~~~~~~~~~^~~~ helper.cpp: In function 'std::vector > parse2str(std::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 306 | for (int i=0 ; i < s.length() ; i++) | ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 307 | if (s[i] == ',' || i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ helper.cpp:309:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 309 | if (i == s.length()-1) t += s[i]; | ~~^~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector parse2int(std::string)': helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 323 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In member function 'void CArgs::check_unused_options(Plink&)': helper.cpp:461:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 461 | for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 659 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 664 | for (int i=0;i > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 709 | while(h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 729 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 775 | for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 795 | for (int s = 0 ; s < snps.size() ; s++) | ~~^~~~~~~~~~~~~ helper.cpp: In function 'std::string chromosomeName(int)': helper.cpp:952:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 952 | if ( c < 0 || c >= par::chr_code.size() ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'int getMarkerChromosome(Plink&, std::string)': helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 959 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 966 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 973 | for (int l=0;l getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 989 | for (int i=0;i getChromosomeRange(Plink&)': helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1040 | for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1264 | if (sample[i]->fid.length() > par::pp_maxfid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1267 | if (sample[i]->iid.length() > par::pp_maxiid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1273 | if (locus[l]->name.length() > par::pp_maxsnp) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ plink.cpp: In function 'int main(int, char**)': plink.cpp:763:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 763 | par::make_founders && | ~~~~~~~~~~~~~~~~~~~^~ 764 | !par::built_families) | ~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1391 | for (int j=0; jfreq * ( 1 - locus[l]->freq ); | ^~ In file included from tinput.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] 843 | double e10 = E10*S; | ^~~ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] 844 | double e20 = E20*S; | ^~~ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] 848 | double e21 = E21*S; | ^~~ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 1067 | if ( (!par::silent ) && c==c2 || c==np) | ~~~~~~~~~~~~~~~~^~~~~~~~ helper.cpp: In member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; | ^ helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2455 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2462 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2491 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2510 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2530 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2549 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2568 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2106 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2587 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2606 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 246 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 256 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 271 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 309 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2638 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1227 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 591 | if ( c > sample.size()) | ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 603 | if ( gn != 2 * sample.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~ plink.cpp: In member function 'void Plink::cleanUp()': plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2359 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2362 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2366 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2671 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2722 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2756 | for (int j=1; j, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2935 | for (int i=0; i&)': helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2959 | if ( input.size() != P.nl_all ) | ~~~~~~~~~~~~~^~~~~~~~~~~ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] 458 | int m,l,iter,i,k; | ^ stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] 813 | const double eps = 1e-12; | ^~~ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] 818 | int r = u.size(); | ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] 906 | const double eps = 1e-12; | ^~~ helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; | ^ stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1477 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1483 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1515 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1521 | for (int c = 0 ; c < keep.size(); c++) | ~~^~~~~~~~~~~~~ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1531 | for (int i = 0; i < v.size(); i++) | ~~^~~~~~~~~~ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] 3324 | int last = -1; | ^~~~ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] 3328 | int thisChromosome = P.locus[0]->chr; | ^~~~~~~~~~~~~~ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] 3329 | int nextChromosome; | ^~~~~~~~~~~~~~ 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 helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] 218 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'int CArgs::value_int(std::string)': helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] 231 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] 243 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'double CArgs::value_double(std::string)': helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] 255 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'int getInt(std::string, std::string)': helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'double getDouble(std::string, std::string)': helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from stats.h:19, from stats.cpp:24: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool svdcmp(std::vector >&, std::vector&, std::vector >&)' at stats.cpp:1150:15: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'nm' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ stats.cpp: In function 'bool svdcmp(std::vector >&, std::vector&, std::vector >&)': stats.cpp:1035:22: note: 'nm' was declared here 1035 | int i,its,j,jj,k,l,nm; | ^~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 95 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 123 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 132 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 155 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 163 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 198 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 273 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 739 | for ( int l = 0 ; l < locus.size() ; l++ ) | ~~^~~~~~~~~~~~~~ filters.cpp:762:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 762 | for ( int i = 0 ; i < sample.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1078 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1091 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1143 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1165 | for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 295 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 304 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 357 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 372 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 190 | for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] 191 | for (int i2=0; i2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mds.cpp:279:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 279 | if ( elist.size() != par::cluster_mds_dim ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] 242 | bool flag = svd(D,eigenvalue,eigenvector); | ^~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 452 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 626 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 648 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 651 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 784 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 84 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 86 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 954 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 955 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 975 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 976 | for (int j=i+1; j::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 990 | (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1038 | for(int j=0;j >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1041 | if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ cluster.cpp:1049:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1049 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1050 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1060 | for (int j1=0; j1 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1061 | for (int j2=0; j2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1107 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1163 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1203 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1204 | for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1228 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1229 | for (int j=0; j&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1254 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1255 | for (int j=0; j&, std::vector&)': cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1272 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1276 | for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1290 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j::iterator loc1 = locus.begin()+m1; | ^~~~ output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] 403 | vector::iterator loc2 = locus.begin()+m2; | ^~~~ cluster.cpp: In member function 'void Plink::groupGenome()': cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1643 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1661 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1664 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 520 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 526 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2200 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2322 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2367 | for (int i=0; i < setname.size();i++) | ~~^~~~~~~~~~~~~~~~ output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2380 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2409 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2412 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | if ( col_length != tokens.size() ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 105 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 741 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 744 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 785 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 788 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ output.cpp: In member function 'void Plink::display_pairList()': output.cpp:145:61: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized] 145 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " " | ~~~~~~~~^~~~~~~~~~~~ output.cpp:116:11: note: 'i2' was declared here 116 | int i1, i2; | ^~ output.cpp:144:61: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] 144 | << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " " | ~~~~~~~~^~~~~~~~~~~~ output.cpp:116:7: note: 'i1' was declared here 116 | int i1, i2; | ^~ In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 146 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] 154 | for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int e=0;e >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 226 | if (len != tokens.size() - offset ) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ prephap.cpp:283:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 283 | for ( int i = allele ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ prephap.cpp:412:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 412 | while ( index < tokens.size() ) | ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:41: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 416 | if ( tokens[index].size() != len ) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 420 | if ( index == tokens.size() - 1 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 470 | for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 533 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 560 | for (int i=0; i vif_prune(std::vector >, double, std::vector&)': helper.cpp:1405:11: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] 1405 | int maxI; | ^~~~ In file included from phase.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 373 | for (int i=0; i&)': phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 472 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 678 | for (int z=0; z, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1238 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1280 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1299 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) | ~~^~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1829 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1843 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1888 | for (int z = 0; z < h1.size(); z++) | ~~^~~~~~~~~~~ assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1109:68: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] 1109 | pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) ); | ~~~~~^~~~~~~~~~ assoc.cpp:1019:14: note: 'pvalue' was declared here 1019 | double pvalue; | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) | ~~~~^~~~~ input.cpp:60:10: note: 'PED' was declared here 60 | FILE * PED; | ^~~ In file included from /usr/include/c++/12/iostream:39, from assoc.cpp:14: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1590:26: /usr/include/c++/12/ostream:221:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:36: note: 'gen_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1697:26: /usr/include/c++/12/ostream:221:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:25: note: 'rec_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1672:26: /usr/include/c++/12/ostream:221:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:14: note: 'dom_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'std::vector Plink::fullModelAssoc(bool, Perm&)' at assoc.cpp:1647:26: /usr/include/c++/12/ostream:221:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1385:22: note: 'mult_chisq' was declared here 1385 | double mult_p, mult_chisq; | ^~~~~~~~~~ In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 91 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 258 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:272:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ trio.cpp:335:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 335 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 342 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp:350:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 350 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 469 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 474 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 492 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 504 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 871 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 882 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 895 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 936 | for (int f=0;f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 943 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:13: warning: unused variable 'tmp' [-Wunused-variable] 962 | int tmp = deleteIndividuals(indel); | ^~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1038 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1048 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1236 | for ( int k=0; kpm->kids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1245 | 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:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 81 | for (int i=0; iperson.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:30: warning: unused variable 'person' [-Wunused-variable] 96 | Individual * person = klist[k]->person[i]; | ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 132 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | for (int c=0; c < fam->kid.size(); c++) | ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 234 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 327 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 412 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 415 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 522 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 557 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 776 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 145 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 187 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 199 | for(int i=0; i&, std::vector&)': perm.cpp:273:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 273 | for (int j=0;j< P.pS->snpset[l].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 37 | for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 52 | for(int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 59 | else if (par::set_min > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:48: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 62 | if (par::set_max==-1 || par::set_max > snpset[i].size() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 99 | for(int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 129 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 216 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 236 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 237 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 317 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 323 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 329 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 332 | for (int k=j+1; k < snpset[i].size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 367 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 370 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 412 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 618 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 631 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 632 | for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 642 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 643 | for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 703 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:713:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 713 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 975 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1042 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 489 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 497 | for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1025 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1033 | for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] 1198 | bool casewise_deletion = false; | ^~~~~~~~~~~~~~~~~ In file included from perm.h:17, from genedrop.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 64 | for (int i=0; i&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int k=0; kkids.size(); k++) | ~^~~~~~~~~~~~~~~~~~~~ In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1249 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -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 merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 333 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 377 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 403 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 426 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 733 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 784 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 830 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 842 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 77 | if (!sample[i]->missing) | ^ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 173 | for (int s=0; s::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'void CCA_logit(bool, std::vector >&, Set&, Plink&)' at genepi.cpp:855:84: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:614:17: note: 'cancor1_pos' was declared here 614 | int cancor1_pos; | ^~~~~~~~~~~ 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 helper.h:24, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 85 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 131 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)': haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 62 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:79:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 79 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 93 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] 268 | double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); | ^ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 357 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ haploCC.cpp:375:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 375 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ merge.cpp: In member function 'bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] 1103 | if (write) | ^~ merge.cpp:943:8: note: 'write' was declared here 943 | bool write; | ^~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.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 webcheck.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 qfam.cpp In file included from haploTDT.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 117 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 130 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 146 | if ( i < tokens.size()-1 ) | ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 180 | if ( i < tokens.size() - 1) | ~~^~~~~~~~~~~~~~~~~~~ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 93 | for (int f=0; f > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 195 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 198 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 293 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 328 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 97 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 267 | for (int i=0; i < family.size(); i++) | ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 315 | 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:505:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 505 | for ( int k = 0 ; k < (*f)->kid.size() ; k++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 648 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 657 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 50 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] 90 | long int inc; | ^~~ bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 357 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 390 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 409 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 417 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 440 | for (int i=0; isecond; | ^~~~ bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 697 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 839 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 871 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 883 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 236 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 349 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 373 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from parse.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from /usr/include/c++/12/vector:64, from linear.h:17, from linear.cpp:18: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = std::vector; _Alloc = std::allocator >]', inlined from 'void gaussj(matrix_t&, matrix_t&)' at linear.cpp:97:36: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:75:14: note: 'irow' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = std::vector; _Alloc = std::allocator >]', inlined from 'void gaussj(matrix_t&, matrix_t&)' at linear.cpp:102:15: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:75:9: note: 'icol' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ 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 legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 368 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 377 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 381 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 384 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 390 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 415 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 424 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 460 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 461 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 462 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 467 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 480 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 673 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 695 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | for (int i=0; i < plist.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 logistic.cpp homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 756 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 773 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 861 | for (int i=0; i < plist.size(); i++) | ~~^~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1178 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1331 | for (int i=0; i< (*pA)->segs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1437 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1441 | if ( (*pA)->match[i].size() >= maxlist ) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1461 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; 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 model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from model.cpp:17: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from plink.h:21, from legacy.cpp:21: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Locus*; _Alloc = std::allocator]', inlined from 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)' at legacy.cpp:206:51: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': legacy.cpp:35:7: note: 'last' was declared here 35 | int last; | ^~~~ model.cpp: In member function 'void Model::setMissing(std::vector&)': model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 132 | if ( include.size() != P->n ) | ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 354 | for (int i=0; i< par::parameter_list.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 367 | for ( int i = 0 ; i < X.size() ; i++) | ~~^~~~~~~~~~ model.cpp:374:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 374 | for ( int j = 0 ; j < par::parameter_list.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] 613 | double maxVIF = 0; | ^~~~~~ In file included from helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 871 | if (!ibd) | ^~ segment.cpp:875:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 875 | SIBS << setw(10) << original[l] << " " | ^~~~ segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:22: warning: unused variable 'p1' [-Wunused-variable] 954 | Individual * p1 = sample[i1]; | ^~ segment.cpp:955:22: warning: unused variable 'p2' [-Wunused-variable] 955 | Individual * p2 = sample[i2]; | ^~ segment.cpp:1027:26: warning: unused variable 'p1' [-Wunused-variable] 1027 | Individual * p1 = sample[i1]; | ^~ segment.cpp:1028:26: warning: unused variable 'p2' [-Wunused-variable] 1028 | Individual * p2 = sample[i2]; | ^~ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] 950 | int c=0; | ^ segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; ifirst; | ^ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] 2003 | int nseg = smap.size(); | ^~~~ segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2378 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2380:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2380 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2382:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2382 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2412:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2412 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2414:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2414 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2416:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2416 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2443:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2443 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2445:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2445 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2447:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2447 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2474:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2474 | else if ( par::cnv_col = 1 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2476:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2476 | else if ( par::cnv_col = 2 ) | ~~~~~~~~~~~~~^~~ segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2478 | else if ( par::cnv_col = 3 ) | ~~~~~~~~~~~~~^~~ In file included from helper.h:24, from glm.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] 849 | error("Internal problem with QFAM model specification"); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from glm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 294 | for (int h=1; h < whap->current->group.size(); h++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 423 | for (int c=0; c *xn)) goto S160; | ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 3544 | if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 6025 | if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6088 | qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; | ~~~~~~^~~~~~~~~~~~~ dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6112 | qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6153 | qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; | ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; | ^~~ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 6401 | if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 6782 | if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 6996 | qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ glm.cpp:610:35: warning: 'df' may be used uninitialized [-Wmaybe-uninitialized] 610 | double pvalue = chiprobP(chisq,df); | ~~~~~~~~^~~~~~~~~~ glm.cpp:556:15: note: 'df' was declared here 556 | int df; | ^~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.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 dfam.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 fisher.cpp In file included from helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 493 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 609 | for (int l=0; l< original.size(); l++) | ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] 654 | const double pthresh = 0.01; | ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] 655 | bool one_sided = true; | ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] 707 | int srange_cnt = 0; | ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] 708 | bool inRange = false; | ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 895 | for (int i = 0 ; i < tokens.size() ; i++) | ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 86 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 96 | for ( int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~~ dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 106 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 271 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 378 | for (int c=0; ckid.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:16: warning: unused variable 'informative' [-Wunused-variable] 218 | bool informative = false; | ^~~~~~~~~~~ dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 504 | for (int c=0; cperson.size(); c++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 68 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 128 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 136 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 146 | for (int l=0; l< locus.size(); l++) | ~^~~~~~~~~~~~~~ linput.cpp:164:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 164 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 200 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 209 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::string, int, std::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] 78 | char out_buf[BUF_SIZE+1]; // Output buffer for GET request | ^~~~~~~ sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] 79 | char in_buf[BUF_SIZE+1]; // Input buffer for response | ^~~~~~ sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] 81 | unsigned int i; // Loop counter | ^ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] 119 | int echoStringLen = 100; | ^~~~~~~~~~~~~ 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 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 proxy.cpp elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:374:10: warning: 'wt' may be used uninitialized [-Wmaybe-uninitialized] 374 | double wt; | ^~ In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 206 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 289 | for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 314 | for (int i=1; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 332 | if ( added.size() >= par::proxy_snp_filter ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 854 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1332 | for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1401 | for (int c1 = 0; c1 < collection.size() ; c1++ ) | ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:19: warning: unused variable 't1' [-Wunused-variable] 1448 | int t1=0; | ^~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] 169 | CSNP * s = SNP[l]; | ^ In file included from pdriver.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from haploQTL.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)': haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1142:18: warning: 'p_gcnt' may be used uninitialized [-Wmaybe-uninitialized] 1142 | ++(*p_gcnt); | ~^~~~~~~~ elf.cpp:1112:13: note: 'p_gcnt' was declared here 1112 | int * p_gcnt; | ^~~~~~ elf.cpp:1147:22: warning: 'p_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1147 | ++(*p_cnt); | ~^~~~~~~ elf.cpp:1111:13: note: 'p_cnt' was declared here 1111 | int * p_cnt; | ^~~~~ 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 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 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 nonfounderphasing.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 134 | for (int l=0; l < actual_map.size(); l++) | ~~^~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 297 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 337 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 396 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] 487 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 655 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 754 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 802 | for (int z=0; z::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 850 | if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 851 | ||alleles2.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 957 | if (mask1.size() != ns ||alleles1.size() != ns ) | ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1225 | for (int z = 0; z < hap1[p1].size(); z++) | ~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1251 | for (int z1 = 0; z1 < hap1[p1].size(); z1++) | ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1252 | for (int z2 = 0; z2 < hap1[p2].size(); z2++) | ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] 1250 | int j=0; | ^ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1419 | for( int z = 0; z < pp[i].size(); z++ ) | ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1477 | for( int z = 0; z < pp[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 clumpld.cpp haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 683 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 691 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 751 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 791 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 798 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 868 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 872 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 949 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 966 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::phaseAndScoreNonfounder(int)': nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) | ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] 360 | int pcnt=1; | ^~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 92 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 128 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 137 | for ( int f=0; f >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 173 | if ( tokens.size() <= snp_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 201 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) | ~~^~~~~~~~~~~ clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 480 | if( l1 < P->locus.size()-1 ) | ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 520 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int f=1; f<=filename.size(); f++) | ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1097 | if( j < grouped_snps.size()-1) | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp 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 genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from options.h:18: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'void Plink::performProxyTests(int)' at proxy.cpp:932:43: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ proxy.cpp: In member function 'void Plink::performProxyTests(int)': proxy.cpp:422:7: note: 'ref' was declared here 422 | int ref; | ^~~ In file included from em.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 97 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 106 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 128 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 132 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 162 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 166 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 189 | for( int a = 0; a < posshap1.size(); a++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 190 | for( int b = 0; b < posshap2.size(); b++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 225 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 315 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 328 | for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] 347 | for (int z = 0; z < new_hap1.size(); z++) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 358 | for (int z2=0; z2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 105 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] 304 | bool OLD_clist = par::clist; | ^~~~~~~~~ profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] 350 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] 351 | double pvalue = pval[ pval.size()-1 ]; | ^~~~~~ profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] 352 | double beta = b[ b.size()-1 ]; | ^~~~ profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 390 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 402 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 421 | if ( qcnt == qlabel.size() ) | ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:16: warning: unused variable 'a1' [-Wunused-variable] 480 | bool a1 = i2->second; | ^~ profile.cpp:525:16: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] 525 | bool sawNamedAllele = false; | ^~~~~~~~~~~~~~ profile.cpp:629:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 629 | for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 667 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 107 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 124 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 151 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 160 | for (int i=0; i > NList::tokenize(std::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 189 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 239 | if ( s[i]== range_char && i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | 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 simul.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 gvar.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] 172 | double gh_11_12 = h11*h12; | ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 679 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs_QT()': simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 393 | for (int g=0; g::size_type' {aka 'long unsigned int'} [-Wsign-compare] 454 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 456 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int s=0; s < conditioner.size(); s++) | ~~^~~~~~~~~~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 793 | if ( p1 != coeff1.size() || p0 != coeff0.size() ) | ~~~^~~~~~~~~~~~~~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 962 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 986 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1015 | for (int i=0; i< tok.size(); i++) | ~^~~~~~~~~~~~ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1048 | for ( int i = 0 ; i < tok.size() ; i++ ) | ~~^~~~~~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1118 | if ( mapping.size() != H->ns + H->nh ) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1129 | for (int i=0; i< lst.size(); i++) | ~^~~~~~~~~~~~ whap.cpp:1142:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1142 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1162 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1197 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1231 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1290 | for (int g=0; g< model.group.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~ whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1326 | for (int c=0; c < P->conditioner.size(); c++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1334 | for (int l=0; l&, ChapModel&)': whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1425 | for (int h=0; h < m.group.size(); h++) | ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1434 | if ( cnt>0 && cnt2 < m.group[h].size() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ 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 gvar.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 125 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 192 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 247 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 298 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 381 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 403 | for (int i=0; isecond; | ^~ gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] 414 | bool fatal = false; | ^~~~~ gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 549 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 556 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:247:18: warning: unused variable 'p2' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:332:19: warning: unused variable 'p1' [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 815 | for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] 825 | for (int s2=s1+1; s2::iterator i2 = isection.begin(); | ^~ cnv.cpp:1103:43: warning: variable 'il' set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] 412 | int nseg=0; | ^~~~ cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; | ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2013 | for (int c = 0 ; c < scaffold.size(); c++) | ~~^~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] 2098 | noCovar == true; | ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] 2202 | indivPair p = ic->first; | ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] 2288 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] 2289 | double pvalue = pval[ pval.size()-1 ]; | ^~~~~~ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 147 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 148 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 156 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 169 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 240 | for (int l=0; l< ari->second.size(); l+=2) | ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] 125 | int cnt = 0; | ^~~ 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:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | 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] 122 | long int nfound = 0; | ^~~~~~ In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp 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 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 cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 237 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 263 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from idhelp.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 110 | if ( tokens.size() != cols ) | ~~~~~~~~~~~~~~^~~~~~~ setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 188 | for ( int j = 0; j < pS->snpset.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int i=0; i < snpset[j].size(); i++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 40 | for ( int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 63 | for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 136 | for (int g=0; gvalues.size(); g++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::map >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 169 | if ( found != matchTemplate.size() ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] 128 | bool match = true; | ^~~~~ idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 296 | for ( int i = 0 ; i < mask.size() ; i++) | ~~^~~~~~~~~~~~~ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] 214 | vector & jo = jointOrder[j]; | ^~ idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 346 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 502 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 510 | if ( p < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 542 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 547 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 553 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:529:24: warning: unused variable 'seenJoint' [-Wunused-variable] 529 | bool seenJoint = true; | ^~~~~~~~~ idhelp.cpp:584:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 584 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ idhelp.cpp:594:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 594 | for (int i = 0 ; i < ids.size() ; i++) | ~~^~~~~~~~~~~~ In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 678 | if ( ++p == tokens.size() ) | ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 727 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 742 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 745 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:747:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 757 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] 744 | set & jf = jointField[j]; | ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 772 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 790 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 794 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 836 | for (int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 888 | if ( tokens.size() != file->uniqFieldCount ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:38: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 894 | int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 903 | if ( j < tokens.size() ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 922 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 950 | for ( int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 975 | if ( v->value.size() + 3 > myField->width ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1000 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1003 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1013 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] 1015 | IDGroup * group = idgroup[g]; | ^~~~~ idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1025 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1028 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:21: warning: unused variable 'v' [-Wunused-variable] 1031 | IDValue & v = *(group->values[j]); | ^ idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1070 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1085 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1128 | for ( int k = 0; k < (*i0)->values.size(); k++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1183 | for (int z=0; zvalues.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:46: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1189 | for (int z=0; z<(*i0)->values.size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1236 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1242 | for (int j = 0 ; j < group->values.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:21: warning: unused variable 'v' [-Wunused-variable] 1245 | IDValue & v = *(group->values[j]); | ^ idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1346 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1424 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1440 | for ( int j = 0; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1551 | for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1631 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1648 | for (int f = 0 ; f < targetFields.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1649 | for (int i = 0 ; i < tokens.size(); i++) | ~~^~~~~~~~~~~~~~~ idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1654 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1675 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1684 | if ( tokens.size() <= maxfield ) | ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1692 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1710 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1733 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1735 | for (int i = 0 ; i < thisGroup->values.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1770 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1784 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1801 | for (int i = 0 ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1856 | for (int s=0; s< par::idhelp_match_string.size(); s+=2) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1903 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1937 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1957 | for (int f = 0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1964 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1986 | for (int f = 0 ; f < fieldNames.size(); f++) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:29: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 2018 | if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2024 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2030 | if ( maxF >= tok.size() ) | ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2034 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2070 | for (int v=0; vvalues.size(); v++) | ~^~~~~~~~~~~~~~~~~ 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 g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] 1889 | bool jointQuery = id.find("+") != string::npos; | ^~~~~~~~~~ idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2167 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2168 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2201 | for (int k = 0 ; k < thisLine.size() ; k++ ) | ~~^~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2229 | for ( int g = 0 ; g < idgroup.size(); g++ ) | ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2234 | for (int j = 0 ; j < group->values.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 163 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 203 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 280 | for (int i = 0 ; i < ids.size(); i++) | ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 325 | for (int t = 0 ; t < tokens.size() ; t++) | ~~^~~~~~~~~~~~~~~ In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; | ^~~~~ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] 156 | int numStrong = 0; | ^~~~~~~~~ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] 157 | int numRec = 0; | ^~~~~~ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] 158 | int numInGroup = 0; | ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] 226 | int cnt = 0; | ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 418 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 427 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ blox.cpp:569:41: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] 569 | if ( pB1>0 ) loglike1 += knownBA * log( pB1 ); | ~~~^~~~~~~ blox.cpp:489:22: note: 'pB2' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:505:10: warning: 'pB1' may be used uninitialized [-Wmaybe-uninitialized] 505 | double p1 = pA1 + pB1; | ^~ blox.cpp:489:18: note: 'pB1' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:503:10: warning: 'pA2' may be used uninitialized [-Wmaybe-uninitialized] 503 | double pA = pA1 + pA2; | ^~ blox.cpp:489:14: note: 'pA2' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ blox.cpp:510:10: warning: 'pA1' may be used uninitialized [-Wmaybe-uninitialized] 510 | double D = pA1 - (pA*p1); | ^ blox.cpp:489:10: note: 'pA1' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 513 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 548 | for (int f = 0 ; f < vzin.size() ; f++ ) | ~~^~~~~~~~~~~~~ dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 581 | if ( tok.size() < firstCol ) | ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 601 | for (int i=firstCol; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 695 | for (int i = 0; i < personMap[f].size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 750 | if ( tok.size() != expected[f] ) dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ dosage.cpp:1170:18: warning: unused variable 'statistic' [-Wunused-variable] 1170 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1252 | if ( o->second != dosageFilename_all.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1310 | if ( ++qq == qthresh.size() ) | ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] 190 | int geno_field = a2_field + skip2 + 1; | ^~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 149 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 250 | if ( tokens.size() <= chr_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 251 | tokens.size() <= bp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 260 | if ( tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 275 | if ( tokens.size() <= snp_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:16: warning: unused variable 'include' [-Wunused-variable] 300 | bool include = false; | ^~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.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 r.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 Rconnection.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 zfstream.cpp In file included from Rconnection.h:42, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ In file included from Rconnection.h:42, from Rconnection.cpp:30: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 203 | { name=""; fix_content(); } | ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 206 | { name=""; fix_content(); } | ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } | ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] 245 | while (i < len) { if (!c[i]) nel++; i++; } | ~~^~~~~ Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ | ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 567 | if (host) free(host); host=0; | ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 567 | if (host) free(host); host=0; | ^~~~ In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor 'Alleles::Alleles(std::string, int, int, std::string, std::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] 47 | int bp; | ^~ metaanal.cpp:44:10: warning: 'std::string Alleles::a1' [-Wreorder] 44 | string a1; | ^~ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] 61 | Alleles(string name, int chr, int bp, string a1, string a2) | ^~~~~~~ metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 159 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 182 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 213 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 235 | for (int f = 0 ; f < par::meta_files.size() ; f++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 300 | if ( tokens.size() != fsize ) | ~~~~~~~~~~~~~~^~~~~~~~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 203 | { name=""; fix_content(); } | ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 206 | { name=""; fix_content(); } | ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 232 | char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } | ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] 245 | while (i < len) { if (!c[i]) nel++; i++; } | ~~^~~~~ Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 249 | while (i < nel) { | ~~^~~~~ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:15: warning: unused variable 'ct' [-Wunused-variable] 330 | int ct = data->length(); | ^~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] 253 | int pval_column = -1; | ^~~~~~~~~~~ metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 482 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 637 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 680 | for (int f=0; f::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = CSNP*; _Alloc = std::allocator]', inlined from 'void Plink::processDosageFile()' at dosage.cpp:915:21: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ dosage.cpp: In member function 'void Plink::processDosageFile()': dosage.cpp:725:15: note: 'snp_code' was declared here 725 | int snp_code; | ^~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with '-fvar-tracking-assignments', retrying without 80 | void setOptions(CArgs & a) | ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz make[2]: Leaving directory '/build/plink-1.07+dfsg' make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/plink/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/build/plink-1.07+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_arm64.deb'. dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../plink_1.07+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../plink_1.07+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload 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/29555 and its subdirectories I: Current time: Fri May 5 14:47:51 -12 2023 I: pbuilder-time-stamp: 1683341271 Sat May 6 02:48:01 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Sat May 6 02:48:01 UTC 2023 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Sat May 6 03:30:34 UTC 2023 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Sat May 6 03:30:35 UTC 2023 I: plink_1.07+dfsg-4_arm64.changes: Format: 1.8 Date: Sun, 31 Oct 2021 21:01:46 +0530 Source: plink Binary: plink plink-dbgsym Architecture: arm64 Version: 1.07+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: plink - whole-genome association analysis toolset Closes: 984293 Changes: plink (1.07+dfsg-4) unstable; urgency=medium . * Team upload. * Add patch to fix FTBFS with gcc-11 (Closes: #984293) * Bump Standards-Version to 4.6.0 (no changes needed) * Bump debhelper compatibility level to 13 * Replace ADTTMP with AUTOPKGTEST_TMP * Add "Rules-Requires-Root: no" Checksums-Sha1: 6d3b36e58e41f873e7eb5889dfa6e14b2b72ae2d 26597632 plink-dbgsym_1.07+dfsg-4_arm64.deb bbe626023e2b645a36ae55aba00aa4297d72316e 5172 plink_1.07+dfsg-4_arm64.buildinfo 31ee7ae2823054b91cd7c9fd0721b225913aa3e5 1066572 plink_1.07+dfsg-4_arm64.deb Checksums-Sha256: 22c65ae82010baba88bc7973e525a5ab506fa26bf9ed8e76af9245cad22caf11 26597632 plink-dbgsym_1.07+dfsg-4_arm64.deb 63ca8105937ac367ed0fd14a019b7f2598b3750a44b6546a3f684189be6572b2 5172 plink_1.07+dfsg-4_arm64.buildinfo 15f0517666762b8d6565e1dc7437e1b7f277136b129adf7aa16a5575a2666b55 1066572 plink_1.07+dfsg-4_arm64.deb Files: 0d03bd87647122f7f029f84210ee58da 26597632 debug optional plink-dbgsym_1.07+dfsg-4_arm64.deb fe0d28d318799838a269c4bd49171b95 5172 science optional plink_1.07+dfsg-4_arm64.buildinfo 362a5e6dfd9c695788e5ce61edb1b9fb 1066572 science optional plink_1.07+dfsg-4_arm64.deb Sat May 6 03:30:36 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/plink_1.07+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/plink_1.07+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/plink_1.07+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/b1/plink_1.07+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VTBpSLxw/b2/plink_1.07+dfsg-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.634s) 0.634s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.310s) 0.310s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat May 6 03:30:37 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sat May 6 03:30:37 UTC 2023 I: plink from bookworm built successfully and reproducibly on arm64. Sat May 6 03:30:39 UTC 2023 I: Submitting .buildinfo files to external archives: Sat May 6 03:30:39 UTC 2023 I: Submitting 8.0K b1/plink_1.07+dfsg-4_arm64.buildinfo.asc Sat May 6 03:30:39 UTC 2023 I: Submitting 8.0K b2/plink_1.07+dfsg-4_arm64.buildinfo.asc Sat May 6 03:30:40 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 6 03:30:40 UTC 2023 I: Done submitting .buildinfo files. Sat May 6 03:30:40 UTC 2023 I: Removing signed plink_1.07+dfsg-4_arm64.buildinfo.asc files: removed './b1/plink_1.07+dfsg-4_arm64.buildinfo.asc' removed './b2/plink_1.07+dfsg-4_arm64.buildinfo.asc'