I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 2 18:01:08 +14 2025 I: pbuilder-time-stamp: 1751428868 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [plink_1.07+dfsg-4.dsc] I: copying [./plink_1.07+dfsg.orig.tar.xz] I: copying [./plink_1.07+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Oct 31 15:36:45 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting plink in plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/36842/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 2 04:01 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/36842/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/36842/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=e945599ca60f4b8c930ebdf566a96522 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=36842 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gKnoSIj7/pbuilderrc_SjkZ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gKnoSIj7/b2 --logfile b2/build.log plink_1.07+dfsg-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/36842/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: amd64 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 ... 19716 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} 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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After unpacking 74.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-2 [94.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Fetched 19.9 MB in 2s (10.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19716 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.1-2_amd64.deb ... Unpacking bsdextrautils (2.40.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg-2_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../29-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-2) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... 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: user script /srv/workspace/pbuilder/36842/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/36842/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/plink-1.07+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../plink_1.07+dfsg-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 amd64 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 -j42 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make -j42 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp 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 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 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from informative.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 webcheck.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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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) | ~~^~~~~~~~~~~~~~~~~~~ In file included from bmerge.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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 64 | 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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ informative.cpp:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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&, 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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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 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++) | ~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 126 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 186 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 261 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 339 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 351 | while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 398 | for(int l=0; l < locus.size(); l++) | ~~^~~~~~~~~~~~~~ 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] 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp:611:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~~ sets.cpp: In member function 'void Set::sizeSets()': sets.cpp:37:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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() ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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] 99 | 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] 695 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneMC(Plink&, bool, double)': sets.cpp:129:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 129 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 409 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp:417:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 417 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ sets.cpp:176:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 440 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 216 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 218 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from linear.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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.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 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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 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] 377 | for (int l=0; l >::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++) | ~~^~~~~~~~~~~~~~~~~~ multi.cpp:304:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 304 | for (int i=0;isecond; | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ multi.cpp:357:22: 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ merge.cpp:395:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 395 | for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] 697 | while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 372 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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++) | ~~^~~~~~~~~~~~~~~~~~ merge.cpp:403:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 403 | for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from 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 'bool Plink::readClusterFile(bool)': input.cpp:787:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 787 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 426 | for (int i=0; i >::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++) | ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp:692:14: warning: unused variable 'snp' [-Wunused-variable] 692 | CSNP * snp; | ^~~ bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 412 | for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 413 | for (int j=0; j < snpset[i].size(); j++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ mishap.cpp: In member function 'void Plink::performMisHapTests()': mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 209 | for (int z = 0 ; z < haplo->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ merge.cpp:722:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 722 | if ( i > include.size()) | ~~^~~~~~~~~~~~~~~~ input.cpp:817:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 817 | if (tokens.size() < 2+par::mult_clst) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ input.cpp:821:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 821 | for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] 733 | if ( gn != 2 * include.size() ) | ~~~^~~~~~~~~~~~~~~~~~~~~ In file included from genepi.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'bool Plink::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] 784 | for (int i=0; i::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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~ merge.cpp:830:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 830 | for (int i=0;i > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 618 | 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] 842 | 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] 961 | else if ( ccount != tokens.size() ) | ~~~~~~~^~~~~~~~~~~~~~~~ sets.cpp:642:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::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'} and 'int' [-Wsign-compare] 965 | if (tokens.size() < 2+par::mult_pheno) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'vector_t Set::profileTestScore()': sets.cpp:703:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 703 | for (int i=0; i::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] 50 | 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] 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] 1335 | 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] 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&, 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&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] 458 | int m,l,iter,i,k; | ^ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 95 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 123 | for (int i=0;i >&)': 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::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 >&)': 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] 190 | for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] 191 | for (int i2=0; i2::size_type' {aka 'long unsigned int'} [-Wsign-compare] 198 | 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++) | ~^~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int z=1; z<=qt.size(); z++) | ~^~~~~~~~~~~ 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(); | ^ epi.cpp:438:26: warning: unused variable 'zero' [-Wunused-variable] 438 | double zero = 0; | ^~~~ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:15: warning: unused variable 'geno_nm' [-Wunused-variable] 99 | int geno_nm = 0; | ^~~~~~~ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] 81 | double tothet = 0; | ^~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~ tdt.cpp:96:30: warning: unused variable 'person' [-Wunused-variable] 96 | Individual * person = klist[k]->person[i]; | ^~~~~~ 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; | ^~~ 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++) | ~~^~~~~~~~~~~~~~~~~ input.cpp:1374:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1374 | else if (tokens.size() != par::clist_number + 2 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:210:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 210 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 234 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 273 | for (int i=0; imissing) | ^ filters.cpp:249:14: warning: unused variable 'freq' [-Wunused-variable] 249 | double freq; | ^~~~ filters.cpp:250:11: warning: unused variable 'nm' [-Wunused-variable] 250 | int nm; | ^~ perm.cpp: In member function 'void Perm::setOriginalRanking(vector_t&)': perm.cpp:187:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 187 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 905 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 199 | for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 327 | for (int j=0; jselectedSNPs[l].size(); j++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 330 | if ( j < pS->selectedSNPs[l].size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ perm.cpp: In member function 'bool Perm::update(std::vector&, 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ 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] 591 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 93 | for (int f=0; f::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 279 | if ( elist.size() != par::cluster_mds_dim ) | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ filters.cpp:611:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; ifreq * ( 1 - locus[l]->freq ); | ^~ sets.cpp:975:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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++) | ~~^~~~~~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] 242 | bool flag = svd(D,eigenvalue,eigenvector); | ^~~~ 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++) | ~^~~~~~~~~~~~~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 193 | for (int t=0; t > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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++) | ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp:195:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::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++) | ~^~~~~~~~~~~~~~~~~~~~~ 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 > 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() ) | ~~~~~~^~~~~~~~~~ cluster.cpp:511:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for (int i=0;i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (r.size() != c) error("Not enough arguments given for option: "+s+" "); | ~~~~~~~~~^~~~ cluster.cpp:492:15: warning: unused variable 'size' [-Wunused-variable] 492 | int size = peeps.size(); | ^~~~ 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 ) | ~~^~~~~~~~~~~~~~~ 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 309 | if (i == s.length()-1) t += s[i]; | ~~^~~~~~~~~~~~~~~ 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 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] 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++ ) | ~~^~~~~~~~~~~~~~~ cluster.cpp:626:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1519 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1538 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 784 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 786 | for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1572 | for (int i=0; i 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'} 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] 252 | for (int i=0; i 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] 334 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 557 | for (int c=0; c&, 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++) | ~~^~~~~~~~~~~~~~~~ tdt.cpp:668:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 776 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1745 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 226 | if (len != tokens.size() - offset ) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1764:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1764 | for (int c=0; csex ) ) | ~~^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:30: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 1067 | if ( (!par::silent ) && c==c2 || c==np) | ~~~~~~~~~~~~~~~~^~~~~~~~ haploCC.cpp:93:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 93 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ poo.cpp:239:10: warning: unused variable 'zt' [-Wunused-variable] 239 | double zt; | ^~ input.cpp: In member function 'void Plink::readSegmentFile(std::ifstream&)': input.cpp:1792:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1792 | 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] 283 | for ( int i = allele ; i < tokens.size() ; i++ ) | ~~^~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 373 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 919 | for (int k=0;k&)': 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] 395 | for (int i=0; iprofileSNPs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1227 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 1078 | for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 975 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 678 | for (int z=0; z >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 976 | for (int j=i+1; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1091 | for (int l=0; l::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; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 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 ) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ 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] 258 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readMapFile(std::string, std::vector&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2116 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 272 | for (int k=0; kkid.size(); k++) | ~^~~~~~~~~~~~~~~ input.cpp:2172:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2172 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1143 | for (int l=0; l::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++) | ~~^~~~~~~~~~~~~~ cluster.cpp:1107:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1107 | for (int i=0; i >&, 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::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1110 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1165 | 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] 335 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp:611:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 611 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1133 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 342 | for ( int k=0; k<(*f)->kid.size(); k++) | ~^~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 1163 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1169 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 340 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~ input.cpp:2397:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2397 | for (int i=0;isex ) ) | ~~^~~~~~~~~~~~~~ genepi.cpp:1044:17: warning: unused variable 'ne' [-Wunused-variable] 1044 | int ne = n1 < n2 ? n1 : n2;// ne = min(p,q) | ^~ genepi.cpp:1064:17: warning: unused variable 'nind' [-Wunused-variable] 1064 | int nind = calcGENEPIMeanVariance(pSNP, | ^~~~ 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~ 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 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haploCC.cpp:392:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 392 | if ( ! ( haploid || X && person->sex ) ) | ~~^~~~~~~~~~~~~~ input.cpp:2419:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2419 | for (int i=0; i&, 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; | ^~~~~~~~~~~~~~~~~ input.cpp:2453:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2453 | for (int i=0; i > 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] 2471 | 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] 785 | for (int i=0;ipv_set.size();i++) | ~^~~~~~~~~~~~~~~~~~ cluster.cpp:1204:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1204 | for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 788 | for (int j=0;jpv_set[i].size();j++) | ~^~~~~~~~~~~~~~~~~~~~~ cluster.cpp: In function 'double groupAvgLink(std::vector >&, 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] 775 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1229 | for (int j=0; j&, 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++) | ~~^~~~~~~~~~~~~ cluster.cpp: In function 'bool homogeneous_clusters(Plink&, std::vector&, 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::iterator loc1 = locus.begin()+m1; | ^~~~ output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] 403 | vector::iterator loc2 = locus.begin()+m2; | ^~~~ cluster.cpp:1291:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1291 | for (int j=0; j, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1187 | if ( nh != hapmap.size() ) | ~~~^~~~~~~~~~~~~~~~ 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] 1238 | for (int z=0; z >::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] 1280 | for (int z=0; z::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] 952 | if ( c < 0 || c >= par::chr_code.size() ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ phase.cpp:1299:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1299 | for (int z=0; z::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] 1643 | for ( int i = 4; 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] 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] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector 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 >::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 >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1172 | for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1264 | if (sample[i]->fid.length() > par::pp_maxfid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1267 | if (sample[i]->iid.length() > par::pp_maxiid) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1273 | if (locus[l]->name.length() > par::pp_maxsnp) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1389 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1391 | for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1575 | for ( int z = 0 ; z < pp[i].size() ; z++ ) | ~~^~~~~~~~~~~~~~ trio.cpp:871:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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++) | ~~^~~~~~~~~~~~~~~ trio.cpp:931:13: warning: unused variable 'tmp' [-Wunused-variable] 931 | int tmp = deleteSNPs(mendel_locus); | ^~~ trio.cpp:936:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 936 | 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++) | ~~^~~~~~~~~~~ In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1249 | for (int i=0; i::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); | ^~~ In file included from plink.cpp:40: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1038 | for (int f=0; f Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] 1536 | int best = 0 ; | ^~~~ trio.cpp:1048:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1048 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int l=0; l::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 member function 'int Plink::deleteSNPs(std::vector&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] 2204 | int i = 0; | ^ 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] 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] 384 | 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] 390 | 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] 395 | 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] 415 | 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] 424 | 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] 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] 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 ) | ~~~~~~~~~~~~~^~~~~~~~~~~ output.cpp: In member function 'void Plink::outputSetFile()': output.cpp:2200:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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++) | ~~^~~~~~~~~~~~~~~~ plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2106 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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, std::set > readRange(std::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] 3097 | set * s; | ^ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp 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 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++) | ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 82 | for (int k=0; k < (*f)->kid.size() ;k++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.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++) | ~~^~~~~~~~~~~~~~ helper.cpp: In member function 'std::string CArgs::value(std::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] 218 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'int CArgs::value_int(std::string)': helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] 231 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::string)': helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] 243 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'double CArgs::value_double(std::string)': helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] 255 | error("Missing an argument for "+s); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 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++) | ~~^~~~~~~~~~~~~~ helper.cpp: In function 'int getInt(std::string, std::string)': helper.cpp:378:58: warning: control reaches end of non-void function [-Wreturn-type] 378 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::string, std::string)': helper.cpp:391:58: warning: control reaches end of non-void function [-Wreturn-type] 391 | error("Not valid integer argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'double getDouble(std::string, std::string)': helper.cpp:404:58: warning: control reaches end of non-void function [-Wreturn-type] 404 | error("Not valid numeric argument for : "+a+" [ "+s+" ]"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1134 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1178 | if ( thispool->segs.size() >= par::pool_size_min ) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1331 | for (int i=0; i< (*pA)->segs.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1437 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 1441 | if ( (*pA)->match[i].size() >= maxlist ) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1461 | for (int i=0; i < (*pA)->group.size() ; i++) | ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value] 2155 | homozygWindows[l] == 0; 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; | ~~~~~~~~~~~~^~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp 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; | ~~~~~~^~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ~~~~~~~~~~~~^~~~~~~~~~~~~~ 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; | ^~~~ 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; | ^~ 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; | ^~~~ 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; | ^ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1529 | for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp segment.cpp: In member function 'void Plink::indivSegmentSummary()': segment.cpp:1855:21: warning: variable 'p' set but not used [-Wunused-but-set-variable] 1855 | indivPair p = ic->first; | ^ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp 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 ) | ~~~~~~~~~~~~~^~~ 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&)': 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 66 | for (int i=0; i >::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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp In file included from glm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 294 | for (int h=1; h < whap->current->group.size(); h++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 344 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 355 | for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] 423 | for (int c=0; c >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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; | ^~ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 493 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 609 | for (int l=0; l< original.size(); l++) | ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] 654 | const double pthresh = 0.01; | ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] 655 | bool one_sided = true; | ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] 707 | int srange_cnt = 0; | ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] 708 | bool inRange = false; | ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 895 | for (int i = 0 ; i < tokens.size() ; i++) | ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 939 | if ( tokens.size() != ncol ) | ~~~~~~~~~~~~~~^~~~~~~ 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 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from sockets.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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] 151 | int totalInformative = 0; | ^~~~~~~~~~~~~~~~ In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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] 206 | for (int i=25; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 209 | for (int i=0; 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, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized [-Wmaybe-uninitialized] 1103 | if (write) | ^~ merge.cpp:943:8: note: 'write' was declared here 943 | bool write; | ^~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.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 haploQTL.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 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from haploQTL.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&, int, bool)': haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 145 | for (int z = 0 ; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ 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 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; | ^~~~~~ output.cpp: In member function 'void Plink::display_indivReport()': output.cpp:69:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized] 69 | << setw(6) << genotype(*this,i1,l) << "\n"; | ~~~~~~~~^~~~~~~~~~~~ output.cpp:46:7: note: 'i1' was declared here 46 | int i1; | ^~ 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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.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++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::reportPhase()': haplohelper.cpp:396:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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] 487 | for (int z = 0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp: In function 'void verboseDisplayWindows2(HaploPhase*, int, bool)': haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 183 | while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 558 | for (int z=0; z < hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 574 | for (int z=0; z < new_pp.size(); z++) | ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 683 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 691 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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'} [-Wsign-compare] 751 | 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 ) | ~~~~~~~~~~~~~~~~^~~~~ haplowindow.cpp:791:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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'} 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 ) | ~~~~~~~~~~~~~~~~^~~~~ haplowindow.cpp: In member function 'void HaploWindow::reportPhase()': haplowindow.cpp:949:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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; | ^ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&)': 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++ ) | ~~^~~~~~~~~~~~~~ In file included from genogroup.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] 1666 | for (int z = 0; z < windows[w]->hap1[r].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp 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] 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp In file included from nonfounderphasing.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 668 | for (int z=0; z < pp[i].size(); z++) | ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] 360 | int pcnt=1; | ^~~~ In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] 715 | double posterior = ip->second; | ^~~~~~~~~ clumpld.cpp: In member function 'std::vector clump_LD::read_assoc_file(std::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 92 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 128 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 137 | for ( int f=0; f >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 173 | if ( tokens.size() <= snp_column || | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 174 | tokens.size() <= pval_column ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 201 | for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] 204 | if ( f < annot_field.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 368 | for (int i = 0; i < sp.size(); i++) | ~~^~~~~~~~~~~ In file included from genoerr.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 157 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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++) | ~~^~~~~~~~~~~~~~~~~ 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp 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::__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++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, 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++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1286:30, inlined from 'void Plink::buildCluster()' at cluster.cpp:128:20: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 437 | __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++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, 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++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1286:30, inlined from 'void Plink::buildCluster()' at cluster.cpp:139:16: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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] 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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from /usr/include/c++/13/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++/13/ostream:223:25: warning: 'mult_chisq' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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++/13/ostream:223:25: warning: 'dom_chisq' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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++/13/ostream:223:25: warning: 'rec_chisq' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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++/13/ostream:223:25: warning: 'gen_chisq' may be used uninitialized [-Wmaybe-uninitialized] 223 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1430:36: note: 'gen_chisq' was declared here 1430 | double dom_chisq, rec_chisq, gen_chisq; | ^~~~~~~~~ In file included from impute.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 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 27 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 34 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 105 | for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | for (int z=0; z< currentWindow->hap1[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 161 | for (int z=0; z< currentWindow->pp[i].size(); z++) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 263 | for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 313 | for (int s=0; s < g.size(); s++) | ~~^~~~~~~~~~ In file included from helper.h:24, from nlist.h:21, from nlist.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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from profile.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 em.cpp:28: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 NList::deparseNumberList(std::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 38 | for (int i=0; i NList::deparseStringList(std::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 83 | for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 107 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 124 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 151 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 160 | for (int i=0; i > NList::tokenize(std::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 189 | for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 239 | if ( s[i]== range_char && i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 253 | else if ( i == s.length()-1 ) | ~~^~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp In file included from helper.h:24, from 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++) | ~~^~~~~~~~~~~~~~~~~~ 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] 635 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 679 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1146 | for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1211 | for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ simul.cpp:1358:30: warning: unused variable 'cumU' [-Wunused-variable] 1358 | double cumA = 0, cumU = 0; | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | for (int g = 0; g < nullModel.group.size(); g++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 393 | for (int g=0; g::size_type' {aka 'long unsigned int'} [-Wsign-compare] 454 | for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] 456 | for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 508 | for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 511 | for ( int g2=0; g2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 619 | if ( g < nullModel.group.size() - 1 ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ gvar.cpp:192:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 192 | for (int l=0; l::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() ) | ~~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::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; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 962 | for (int h=0; hsecond; | ^~ 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] 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++ ) | ~~^~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp 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() ) | ~~~~~^~~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:15: warning: unused variable 'p1' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:247:18: warning: unused variable 'p2' [-Wunused-variable] 247 | int p1,p2; | ^~ cnv.cpp:332:19: warning: unused variable 'p1' [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:332:22: warning: unused variable 'p2' [-Wunused-variable] 332 | int p1,p2; | ^~ cnv.cpp:678:43: warning: variable 'is' set but not used [-Wunused-but-set-variable] 678 | map::iterator is = idescription.find(*ir); | ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 815 | for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] 825 | for (int s2=s1+1; s2::iterator i2 = isection.begin(); | ^~ cnv.cpp:1103:43: warning: variable 'il' set but not used [-Wunused-but-set-variable] 1103 | map::iterator il = segmentLength.find(t); | ^~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] 1414 | int nseg = 1; | ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] 412 | int nseg=0; | ^~~~ cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] 1749 | int cnt = 0; | ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2013 | for (int c = 0 ; c < scaffold.size(); c++) | ~~^~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] 2098 | noCovar == true; | ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] 2202 | indivPair p = ic->first; | ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] 2288 | double statistic = valid ? model->getStatistic() : 0; | ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] 2289 | double pvalue = pval[ pval.size()-1 ]; | ^~~~~~ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] 2290 | double beta = b[ b.size()-1 ]; | ^~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp 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 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] 122 | long int nfound = 0; | ^~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 196 | for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 205 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 221 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 237 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 263 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 276 | for (int j = 0 ; j < inds[i]->kids.size() ; j++) | ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 288 | for (int i = 0 ; i < inds.size() ; i++) | ~~^~~~~~~~~~~~~ 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 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: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++ ) | ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp 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: 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 ) | ~~~~~~~~~~~~~~^~~~~~~ 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++) | ~~^~~~~~~~~~~~ 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: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() ) | ~~~~^~~~~~~~~~~~~~~~ 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:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 727 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 742 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 745 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:747:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 747 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 757 | for ( int j = 0; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] 744 | set & jf = jointField[j]; | ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 772 | for (int j = 0 ; j < jointField.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 790 | for ( int f = 0 ; f < files.size() ; f++ ) | ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 794 | for ( int j = 0 ; j < files[f].fields.size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 808 | for ( int j = 0 ; j < files[f].fields.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp 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() ) | ~~^~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~ 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++) | ~^~~~~~~~~~~~~~~~~ In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: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] 252 | for (int i=0; i >::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 -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp 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 helper.h:24, from zed.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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 252 | for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] 147 | int nsnps = toPosition - fromPosition + 1; | ^~~~~ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] 156 | int numStrong = 0; | ^~~~~~~~~ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] 157 | int numRec = 0; | ^~~~~~ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] 158 | int numInGroup = 0; | ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] 226 | int cnt = 0; | ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 418 | for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] 427 | for (int k=0; k=nel)?0:cont[i]; } | ~^~~~~ blox.cpp: In member function 'void PairwiseLinkage::calculateCI()': blox.cpp:469:7: warning: unused variable 'total_chroms' [-Wunused-variable] 469 | int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH; | ^~~~~~~~~~~~ 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 */ | ^~~~~~~~~~~~~~ In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 567 | if (host) free(host); host=0; | ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 567 | if (host) free(host); host=0; | ^~~~ In file included from 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] 73 | for ( int k = 0 ; k < i->second.size(); k++) | ~~^~~~~~~~~~~~~~~~~~ dosage.cpp: In member function 'void Plink::processDosageFile()': dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 110 | for ( int q = 0 ; q < qthresh.size() ; q++) | ~~^~~~~~~~~~~~~~~~ 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 ) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ 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] ) 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) | ^~~~~~~ dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 989 | for (int q=0; q >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 159 | for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 182 | for (int f=0; fgetStatistic() : 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() ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:213:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 213 | for (int i=0; i::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; | ^~~~~~~~~~ metaanal.cpp:235:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::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 ) | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/c++/13/vector:67, from helper.h:18: In member function 'std::vector::reference std::vector::operator[](size_type) [with _Alloc = std::allocator]', inlined from 'std::vector vif_prune(std::vector >, double, std::vector&)' at helper.cpp:1430:12: /usr/include/c++/13/bits/stl_bvector.h:1087:23: warning: 'maxI' may be used uninitialized [-Wmaybe-uninitialized] 1087 | { return begin()[__n]; } | ~~~~~~~^ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1405:11: note: 'maxI' was declared here 1405 | int maxI; | ^~~~ 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++) | ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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(); | ^~ proxy.cpp:422:7: warning: 'ref' may be used uninitialized [-Wmaybe-uninitialized] 422 | int ref; | ^~~ 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; | ^~~~ 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; | ^~~ input.cpp: In member function 'void Plink::readData()': input.cpp:91:20: warning: 'PED' may be used uninitialized [-Wmaybe-uninitialized] 91 | if ( feof(PED) ) | ~~~~^~~~~ input.cpp:60:10: note: 'PED' was declared here 60 | FILE * PED; | ^~~ dosage.cpp:915:35: warning: 'snp_code' may be used uninitialized [-Wmaybe-uninitialized] 915 | SNP[snp_code]->one[personPosition[f][i]] = s1; | ^ dosage.cpp:725:15: note: 'snp_code' was declared here 725 | int snp_code; | ^~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with '-fvar-tracking-assignments', retrying without 80 | void setOptions(CArgs & a) | ^~~~~~~~~~ g++ -Wall -g -ffile-prefix-map=/build/reproducible-path/plink-1.07+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_amd64.deb'. dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../plink_1.07+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../plink_1.07+dfsg-4_amd64.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: user script /srv/workspace/pbuilder/36842/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/36842/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/36842 and its subdirectories I: Current time: Wed Jul 2 18:02:43 +14 2025 I: pbuilder-time-stamp: 1751428963