Fri Feb 7 06:06:23 UTC 2025 I: starting to build plink/trixie/arm64 on jenkins on '2025-02-07 06:06' Fri Feb 7 06:06:23 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/59282/console.log Fri Feb 7 06:06:23 UTC 2025 I: Downloading source for trixie/plink=1.07+dfsg-4 --2025-02-07 06:06:23-- http://deb.debian.org/debian/pool/main/p/plink/plink_1.07%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... 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% 307M=0s 2025-02-07 06:06:23 (307 MB/s) - ‘plink_1.07+dfsg-4.dsc’ saved [2076/2076] Fri Feb 7 06:06:23 UTC 2025 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----- Fri Feb 7 06:06:23 UTC 2025 I: Checking whether the package is not for us Fri Feb 7 06:06:24 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Feb 7 06:06:24 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Feb 7 06:09:04 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 6 18:06:26 -12 2025 I: pbuilder-time-stamp: 1738908386 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: unsupported subcommand 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/2633583/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='167d9799edc8442dbcffa50ba363fbc1' 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='2633583' 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.JzjSs0ne/pbuilderrc_AuGW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/b1 --logfile b1/build.log plink_1.07+dfsg-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2633583/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 ... 19956 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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{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 21.0 MB of archives. After unpacking 81.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 21.0 MB in 0s (151 MB/s) Preconfiguring packages ... 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 ... 19956 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-2_arm64.deb ... Unpacking bsdextrautils (2.40.4-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-6) ... 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/reproducible-path/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/reproducible-path/plink-1.07+dfsg' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/plink-1.07+dfsg' dh_auto_build -- CXXFLAGS='-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make -j12 "INSTALL=install --strip-program=true" "CXXFLAGS=-Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg' g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from options.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 locus.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 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++) | ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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() ) | ~~~^~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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 genome.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] 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] 787 | 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'} 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] 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++ ) | ~~^~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::readPhenoFile()': input.cpp:897:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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() ) | ~~~~~~~^~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] 391 | double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); | ^~ 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] 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] 1335 | for (int i=0; i::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] 1227 | for (int i=0;i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ genome.cpp:1189:7: warning: unused variable 'win_end' [-Wunused-variable] 1189 | int win_end = win_start + par::prune_ld_win; | ^~~~~~~ filters.cpp: In member function 'void Plink::thinSNPs()': filters.cpp:1277:7: warning: unused variable 'x' [-Wunused-variable] 1277 | int x = 0; | ^ In file included from helper.h:24, from stats.cpp:30: 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: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] 1745 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1764 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1792 | for (int i=0; i&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2200 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2210 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2215 | if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) | ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2225 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2397 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2419 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2453 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2471 | for (int i=0; i&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] 458 | int m,l,iter,i,k; | ^ 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; | ^~~ 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++) | ~~^~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from binput.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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from plink.cpp:28: 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~^~~~~~~~~~ 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 > 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]; | ~~^~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 461 | for (int i=1; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | 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] 659 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 664 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ helper.cpp: In function 'std::vector > 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] 196 | for (int k=0; k::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() ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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] 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 784 | for (int i=0;i 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j 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) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:919:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k::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) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:954:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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 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; 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 >::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] 2106 | for (int i=0;i&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; | ^ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp 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] 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] 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] 2638 | for (int i=0; i >::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] 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 ) | ~~~~~~~~~~~~~^~~~~~~~~~~ helper.cpp: In function 'std::map, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; | ^ 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; | ^~~~~~~~~~~~~~ In file included from mds.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++) | ~~^~~~~~~~~~~~~~~~~~ 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'} 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); | ^~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp In file included from output.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++) | ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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::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; | ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 ; | ^~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp output.cpp: In member function 'void Plink::display_pairList()': output.cpp: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; | ^~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from cluster.cpp:14: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:606:31, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::vector]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp 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 >::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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::map, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~ 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&)': 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++) | ~~^~~~~~~~~~~ tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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 Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1108:11: warning: 'pvalue' may be used uninitialized [-Wmaybe-uninitialized] 1108 | if ( pvalue <= par::set_score_p && pvalue >= 0 ) | ^~ assoc.cpp:1019:14: note: 'pvalue' was declared here 1019 | double pvalue; | ^~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector 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 /usr/include/c++/14/iostream:41, 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:1647:26: /usr/include/c++/14/ostream:229:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] 229 | { 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 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++/14/ostream:229:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] 229 | { 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:1697:26: /usr/include/c++/14/ostream:229:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] 229 | { 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:1590:26: /usr/include/c++/14/ostream:229:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] 229 | { 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; | ^~~~~~~~~ tdt.cpp:936:55: warning: 'zt' may be used uninitialized [-Wmaybe-uninitialized] 936 | double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ; | ~~~^~~~~~~~~~~~~~~~~ tdt.cpp:460:10: note: 'zt' was declared here 460 | double zt; | ^~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp In file included from perm.h:17, from sharing.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++) | ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] 78 | } | ^ genepi.cpp: In function 'long double pillai(int, int, int, double)': genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] 169 | } | ^ genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:28: 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; | ^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp 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] 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] 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from merge.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++) | ~~^~~~~~~~~~~~~~~~~~ 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 >&, Set&, Plink&)': genepi.cpp:840:104: warning: 'cancor1_pos' may be used uninitialized [-Wmaybe-uninitialized] 840 | gene2[i] += (1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp]; | ^ genepi.cpp:614:17: note: 'cancor1_pos' was declared here 614 | int cancor1_pos; | ^~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from hotel.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++) | ~~^~~~~~~~~~~~~~~~~~ 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 >::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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp 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 ) ) | ~~^~~~~~~~~~~~~~ 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, 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; | ^~~~~ In file included from poo.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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 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++) | ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function 'double LinearModel::getPValue()': linear.cpp:734:8: warning: unused variable 'okay' [-Wunused-variable] 734 | bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid; | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from segment.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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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;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 homozyg.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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp 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++) | ~~^~~~~~~~~~~~~~ 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 ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ linear.cpp: In function 'void gaussj(matrix_t&, matrix_t&)': linear.cpp:96:5: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] 96 | if (irow != icol) { | ^~ linear.cpp:75:9: note: 'icol' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ linear.cpp:96:5: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] 96 | if (irow != icol) { | ^~ linear.cpp:75:14: note: 'irow' was declared here 75 | int i,icol,irow,j,k,l,ll; | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)': legacy.cpp:203:32: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 203 | << start - last - 1 << " "; | ~~~~~~^~~~~~ legacy.cpp:35:7: note: 'last' was declared here 35 | int last; | ^~~~ 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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 1882 | if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; | ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 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; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i::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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp 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 /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from bmerge.cpp:14: In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]', inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:634:26, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1294:21, inlined from 'void Plink::mergeBinaryData()' at bmerge.cpp:687:20: /usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'indn' may be used uninitialized [-Wmaybe-uninitialized] 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:682:16: note: 'indn' was declared here 682 | int indn; | ^~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp In file included from helper.h:24, from 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++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~ fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 261 | prterr(1, "NROW must be less than or equal to LDTABL."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:267:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 267 | prterr(2, "All elements of TABLE must be positive."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 272 | prterr(3, "All elements of TABLE are zero.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 273 | "PRT and PRE are set to missing values."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 448 | prterr(1, "NROW must be less than or equal to LDTABL."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 450 | prterr(4, "NCOL must be at least 2"); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:449:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 449 | if (*ncol <= 1) | ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 453 | for (i = 1; i <= *ldkey << 1; ++i) { | ^~~ fisher.cpp:501:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 501 | prterr(2, "All elements of TABLE must be positive."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 508 | prterr(3, "All elements of TABLE are zero.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 509 | "PRT and PRE are set to missing values."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 559 | prterr(5, "The hash table key cannot be computed because " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | "the largest key\n" | ~~~~~~~~~~~~~~~~~~~ 561 | "is larger than the largest representable int.\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | "The algorithm cannot proceed.\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | "Reduce the workspace size, or use `exact = FALSE'."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 750 | prterr(6, "LDKEY is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1538 | prterr(6, "LDKEY is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1539 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:1554:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1554 | prterr(7, "LDSTP is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1555 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1596 | prterr(7, "LDSTP is too small for this problem.\n" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1597 | "Try increasing the size of the workspace."); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2001 | prterr(40, "Out of workspace."); | ^~~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 2078 | prterr(20, "This should never occur."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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; | ^~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from proxy.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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: 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++ ) | ~~^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:28: 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] 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 helper.h:24, from clumpld.h:21, from clumpld.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 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] 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'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) | ~~^~~~~~~~~~~~~~ clumpld.cpp:173:30: warning: comparison of integer expressions of different signedness: 'std::vector >::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 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 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; | ^~~~~~~~~ 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 ) | ~~~^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp 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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp 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 em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 189 | for( int a = 0; a < posshap1.size(); a++ ) | ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:27: 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++) | ~~^~~~~~~~~~ proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] 422 | int ref; | ^~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] 303 | bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ) | ~~^~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 whap.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++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] 172 | double gh_11_12 = h11*h12; | ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 679 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ simul.cpp:1358:30: warning: unused variable 'cumU' [-Wunused-variable] 1358 | double cumA = 0, cumU = 0; | ^~~~ 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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp 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 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; | ^~~ 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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from helper.h:24, from 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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp In file included from setscreen.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++) | ~~^~~~~~~~~~~~~~~~~~ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~ 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: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++ ) | ~~^~~~~~~~~~~~~~~~ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~ 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: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++) | ~~^~~~~~~~~~~~ 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() ) | ~~~~^~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:30: warning: comparison of integer expressions of different signedness: 'std::vector >::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++) | ~^~~~~~~~~~~~~~~~~ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ blox.cpp: In member function 'std::map > 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++) | ~~^~~~~~~~~~~~~~~~~~ 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; qgetStatistic() : 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; | ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp 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; | ^~~ 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: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:565:51: warning: 'pB2' may be used uninitialized [-Wmaybe-uninitialized] 565 | double loglike1 = unknownDH * log( pA1*pB2 + pB1*pA2 ); | ~~~^~~~ blox.cpp:489:22: note: 'pB2' was declared here 489 | double pA1,pA2,pB1,pB2; | ^~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from Rconnection.h:42, from r.cpp:29: Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp] 327 | #warning using little endian based on information from endian.h | ^~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from annot.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/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp 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; | ^~~~~~~ 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 | ^~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~~~ 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 ) | ~~~~~~~~~~~~~~^~~~~~~~ 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 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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(); | ^~ r.cpp:176:17: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 176 | rc->assign("n", rN ); | ~~~~~~~~~~^~~~~~~~~~ r.cpp:68:16: note: 'rc' was declared here 68 | Rconnection *rc; | ^~ r.cpp:376:14: warning: 'rN' may be used uninitialized [-Wmaybe-uninitialized] 376 | delete rN; | ^~ r.cpp:162:14: note: 'rN' was declared here 162 | Rinteger * rN; | ^~ r.cpp:377:14: warning: 'rP' may be used uninitialized [-Wmaybe-uninitialized] 377 | delete rP; | ^~ r.cpp:163:13: note: 'rP' was declared here 163 | Rdouble * rP; | ^~ r.cpp:378:14: warning: 'rS' may be used uninitialized [-Wmaybe-uninitialized] 378 | delete rS; | ^~ r.cpp:164:14: note: 'rS' was declared here 164 | Rinteger * rS; | ^~ r.cpp:380:16: warning: 'rCov' may be used uninitialized [-Wmaybe-uninitialized] 380 | delete rCov; | ^~~~ r.cpp:165:13: note: 'rCov' was declared here 165 | Rdouble * rCov; | ^~~~ In file included from /usr/include/c++/14/vector:66, from options.h:18: In member function 'std::vector<_Tp, _Alloc>::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++/14/bits/stl_vector.h:1131:41: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] 1131 | 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; | ^~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/plink-1.07+dfsg' make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/plink-1.07+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/plink-1.07+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/plink-1.07+dfsg' dh_installexamples chmod 644 debian/plink/usr/share/doc/plink/examples/* make[1]: Leaving directory '/build/reproducible-path/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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_arm64.deb'. dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_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/2633583 and its subdirectories I: Current time: Thu Feb 6 18:09:02 -12 2025 I: pbuilder-time-stamp: 1738908542 Fri Feb 7 06:09:04 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Feb 7 06:09:04 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Feb 7 06:13:46 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Feb 7 06:13:46 UTC 2025 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: 4d5b616a4b49b2ccc9bb531b914d55cd23cbfbb3 25080684 plink-dbgsym_1.07+dfsg-4_arm64.deb 6ebf5bcc5e1f2ba64e66fc2ae51ff7b004c028d4 5054 plink_1.07+dfsg-4_arm64.buildinfo b7b637c0692d0b77f4c987cc3f4dbdf5d5f6dbf0 1107488 plink_1.07+dfsg-4_arm64.deb Checksums-Sha256: 18d046d1c14b5c51b2906da7389ca4e6fdca91212d5eec6a0856183fbd251dc5 25080684 plink-dbgsym_1.07+dfsg-4_arm64.deb 31d807532f4a71e593d640b61105600ff035b793614b28d39f5b8a60695d92a9 5054 plink_1.07+dfsg-4_arm64.buildinfo faf0327932297ab83acf1ffef191b1dce91c864d21d6f0e15bf747fadf97466f 1107488 plink_1.07+dfsg-4_arm64.deb Files: 5cd8570fb6f83f1d660eea72c6c41214 25080684 debug optional plink-dbgsym_1.07+dfsg-4_arm64.deb 42e23c10f9c15c92fb9a180f723850ad 5054 science optional plink_1.07+dfsg-4_arm64.buildinfo 3625e4c653c9e525112a4edc6d915fdc 1107488 science optional plink_1.07+dfsg-4_arm64.deb Fri Feb 7 06:13:48 UTC 2025 I: diffoscope 287 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_9-59282.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/plink_1.07+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/plink_1.07+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/plink_1.07+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/b1/plink_1.07+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.JzjSs0ne/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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 226ms CPU time consumed: 224ms Fri Feb 7 06:13:48 UTC 2025 I: diffoscope 287 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 7 06:13:48 UTC 2025 I: plink from trixie built successfully and reproducibly on arm64. Fri Feb 7 06:13:49 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 7 06:13:49 UTC 2025 I: Submitting 8.0K b1/plink_1.07+dfsg-4_arm64.buildinfo.asc Fri Feb 7 06:13:50 UTC 2025 I: Submitting 8.0K b2/plink_1.07+dfsg-4_arm64.buildinfo.asc Fri Feb 7 06:13:51 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 7 06:13:51 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 7 06:13:51 UTC 2025 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'