sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | plink 1.07+dfsg-2 (armhf) Sun, 05 May 2019 08:21:21 +0000 | +==============================================================================+ Package: plink Version: 1.07+dfsg-2 Source Version: 1.07+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-2e08d045-795d-4eca-a82f-2fd2a429f670' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://debian.oregonstate.edu/debian unstable InRelease Get:2 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8072 kB] Fetched 8072 kB in 2s (3788 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'plink' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/plink.git Please use: git clone https://salsa.debian.org/med-team/plink.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 448 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (dsc) [2077 B] Get:2 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (tar) [429 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (diff) [16.7 kB] Fetched 448 kB in 0s (9858 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/plink-TDJ3lX/plink-1.07+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/plink-TDJ3lX' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-1dkwnk/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-1dkwnk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1dkwnk/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-1dkwnk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1dkwnk/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-1dkwnk/apt_archive ./ Packages [453 B] Fetched 1773 B in 0s (105 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libmpx2-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev autoconf automake libtool flex bison gdb-arm-linux-gnueabihf gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sbuild-build-depends-core-dummy:armhf sensible-utils ucf 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 41.8 MB of archives. After this operation, 152 MB of additional disk space will be used. Get:1 copy:/<>/resolver-1dkwnk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.31.1-16 [2834 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf-base amd64 8.3.0-7cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [6545 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-2 [39.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.28-10cross2 [1172 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:8.3.0-7cross1 [37.1 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 8.3.0-7cross1 [63.2 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 8.3.0-7cross1 [6564 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 8.3.0-7cross1 [301 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 8.3.0-7cross1 [329 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 8.3.0-7cross1 [103 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-armhf-cross all 8.3.0-7cross1 [612 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [6973 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:8.3.0-1 [1456 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 4.19.28-2cross2 [1228 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.28-10cross2 [2149 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-armhf-cross all 8.3.0-7cross1 [1556 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-arm-linux-gnueabihf amd64 8.3.0-7cross1 [7126 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:8.3.0-1 [1180 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.8 MB in 1s (61.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11942 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package binutils-arm-linux-gnueabihf. Preparing to unpack .../06-binutils-arm-linux-gnueabihf_2.31.1-16_amd64.deb ... Unpacking binutils-arm-linux-gnueabihf (2.31.1-16) ... Selecting previously unselected package gcc-8-arm-linux-gnueabihf-base:amd64. Preparing to unpack .../07-gcc-8-arm-linux-gnueabihf-base_8.3.0-7cross1_amd64.deb ... Unpacking gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-7cross1) ... Selecting previously unselected package cpp-8-arm-linux-gnueabihf. Preparing to unpack .../08-cpp-8-arm-linux-gnueabihf_8.3.0-7cross1_amd64.deb ... Unpacking cpp-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Selecting previously unselected package cpp-arm-linux-gnueabihf. Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a8.3.0-1_amd64.deb ... Unpacking cpp-arm-linux-gnueabihf (4:8.3.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-2_all.deb ... Unpacking cross-config (2.6.15-2) ... 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Preparing to unpack .../31-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../32-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../33-libxml-sax-perl_1.00+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.00+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../34-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../35-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../36-libyaml-perl_1.27-1_all.deb ... Unpacking libyaml-perl (1.27-1) ... 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Unpacking crossbuild-essential-armhf (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:armhf. Preparing to unpack .../43-sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.28-10cross2) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-7cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.35-4) ... Setting up libatomic1-armhf-cross (8.3.0-7cross1) ... Setting up libyaml-perl (1.27-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-2) ... Setting up libgcc1-armhf-cross (1:8.3.0-7cross1) ... Setting up gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-7cross1) ... Setting up linux-libc-dev-armhf-cross (4.19.28-2cross2) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-16) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up libgomp1-armhf-cross (8.3.0-7cross1) ... Setting up libc6-dev-armhf-cross (2.28-10cross2) ... Setting up libstdc++6-armhf-cross (8.3.0-7cross1) ... Setting up libubsan1-armhf-cross (8.3.0-7cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up cpp-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan5-armhf-cross (8.3.0-7cross1) ... Setting up libgcc-8-dev-armhf-cross (8.3.0-7cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-armhf-cross (8.3.0-7cross1) ... Setting up gcc-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up gcc-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up g++-8-arm-linux-gnueabihf (8.3.0-7cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-2) ... Setting up dpkg-cross (2.6.15-2) ... Setting up crossbuild-essential-armhf (12.6) ... Setting up sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-1dkwnk/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-1dkwnk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1dkwnk/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-1dkwnk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1dkwnk/apt_archive ./ Sources [485 B] Get:5 copy:/<>/resolver-1dkwnk/apt_archive ./ Packages [570 B] Fetched 2018 B in 0s (117 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:armhf 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-1dkwnk/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:armhf. (Reading database ... 14988 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11), zlib1g-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11), zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-plink-dummy' in '/<>/resolver-1dkwnk/apt_archive/sbuild-build-depends-plink-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-plink-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-1dkwnk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1dkwnk/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-1dkwnk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1dkwnk/apt_archive ./ Sources [639 B] Get:5 copy:/<>/resolver-1dkwnk/apt_archive ./ Packages [720 B] Fetched 2322 B in 0s (124 kB/s) Reading package lists... Reading package lists... Install plink build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db po-debconf zlib1g:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db po-debconf sbuild-build-depends-plink-dummy:armhf zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After this operation, 79.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-1dkwnk/apt_archive ./ sbuild-build-depends-plink-dummy 0.invalid.0 [880 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1 [160 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-1 [1258 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main armhf gcc-8-base armhf 8.3.0-7 [191 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:8.3.0-7 [37.1 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.28-10 [2390 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 8.3.0-7 [339 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 8.3.0-7 [336 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 8.3.0-7 [6740 B] Get:35 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 4.19.28-2 [1140 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.28-10 [2149 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 8.3.0-7 [64.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 8.3.0-7 [103 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-8-dev armhf 8.3.0-7 [611 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-8-dev armhf 8.3.0-7 [1585 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.9 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.8 MB in 0s (51.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14988 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-10_all.deb ... Unpacking libtool (2.4.6-10) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../18-libelf1_0.176-1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../20-libglib2.0-0_2.58.3-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../21-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../22-libncurses6_6.1+20181013-2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2) ... Selecting previously unselected package gettext. Preparing to unpack .../23-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../24-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../25-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../26-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package gcc-8-base:armhf. Preparing to unpack .../27-gcc-8-base_8.3.0-7_armhf.deb ... Unpacking gcc-8-base:armhf (8.3.0-7) ... Selecting previously unselected package libgcc1:armhf. Preparing to unpack .../28-libgcc1_1%3a8.3.0-7_armhf.deb ... Unpacking libgcc1:armhf (1:8.3.0-7) ... Selecting previously unselected package libc6:armhf. Preparing to unpack .../29-libc6_2.28-10_armhf.deb ... Unpacking libc6:armhf (2.28-10) ... Selecting previously unselected package libstdc++6:armhf. Preparing to unpack .../30-libstdc++6_8.3.0-7_armhf.deb ... Unpacking libstdc++6:armhf (8.3.0-7) ... Selecting previously unselected package libasan5:armhf. Preparing to unpack .../31-libasan5_8.3.0-7_armhf.deb ... Unpacking libasan5:armhf (8.3.0-7) ... Selecting previously unselected package libatomic1:armhf. Preparing to unpack .../32-libatomic1_8.3.0-7_armhf.deb ... Unpacking libatomic1:armhf (8.3.0-7) ... Selecting previously unselected package linux-libc-dev:armhf. Preparing to unpack .../33-linux-libc-dev_4.19.28-2_armhf.deb ... Unpacking linux-libc-dev:armhf (4.19.28-2) ... Selecting previously unselected package libc6-dev:armhf. Preparing to unpack .../34-libc6-dev_2.28-10_armhf.deb ... Unpacking libc6-dev:armhf (2.28-10) ... Selecting previously unselected package libgomp1:armhf. Preparing to unpack .../35-libgomp1_8.3.0-7_armhf.deb ... Unpacking libgomp1:armhf (8.3.0-7) ... Selecting previously unselected package libubsan1:armhf. Preparing to unpack .../36-libubsan1_8.3.0-7_armhf.deb ... Unpacking libubsan1:armhf (8.3.0-7) ... Selecting previously unselected package libgcc-8-dev:armhf. Preparing to unpack .../37-libgcc-8-dev_8.3.0-7_armhf.deb ... Unpacking libgcc-8-dev:armhf (8.3.0-7) ... Selecting previously unselected package libstdc++-8-dev:armhf. Preparing to unpack .../38-libstdc++-8-dev_8.3.0-7_armhf.deb ... Unpacking libstdc++-8-dev:armhf (8.3.0-7) ... Selecting previously unselected package zlib1g:armhf. Preparing to unpack .../39-zlib1g_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g:armhf (1:1.2.11.dfsg-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../40-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Selecting previously unselected package sbuild-build-depends-plink-dummy:armhf. Preparing to unpack .../41-sbuild-build-depends-plink-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-plink-dummy:armhf (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up linux-libc-dev:armhf (4.19.28-2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:armhf (8.3.0-7) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:armhf (2.28-10) ... Setting up libc6-dev:armhf (2.28-10) ... Setting up libgcc1:armhf (1:8.3.0-7) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ... Setting up libgomp1:armhf (8.3.0-7) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:armhf (8.3.0-7) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up libstdc++6:armhf (8.3.0-7) ... Setting up debhelper (12.1.1) ... Setting up libasan5:armhf (8.3.0-7) ... Setting up libubsan1:armhf (8.3.0-7) ... Setting up libgcc-8-dev:armhf (8.3.0-7) ... Setting up libstdc++-8-dev:armhf (8.3.0-7) ... Setting up sbuild-build-depends-plink-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.6 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armhf-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armhf-cross_8.3.0-7cross1 linux-libc-dev_4.19.28-2 Package versions: adduser_3.118 apt_1.8.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-arm-linux-gnueabihf_2.31.1-16 binutils-common_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-7 cpp-8-arm-linux-gnueabihf_8.3.0-7cross1 cpp-arm-linux-gnueabihf_4:8.3.0-1 cross-config_2.6.15-2 crossbuild-essential-armhf_12.6 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.6 dpkg-cross_2.6.15-2 dpkg-dev_1.19.6 dwz_0.12-3 e2fsprogs_1.45.0-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1 g++-8_8.3.0-7 g++-8-arm-linux-gnueabihf_8.3.0-7cross1 g++-arm-linux-gnueabihf_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-7 gcc-8-arm-linux-gnueabihf_8.3.0-7cross1 gcc-8-arm-linux-gnueabihf-base_8.3.0-7cross1 gcc-8-base_8.3.0-7 gcc-8-cross-base_8.3.0-7cross1 gcc-arm-linux-gnueabihf_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.0 libarchive-zip-perl_1.64-1 libasan5_8.3.0-7 libasan5-armhf-cross_8.3.0-7cross1 libatomic1_8.3.0-7 libatomic1-armhf-cross_8.3.0-7cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16 libblkid1_2.33.1-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-armhf-cross_2.28-10cross2 libc6-dev_2.28-10 libc6-dev-armhf-cross_2.28-10cross2 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-7 libcom-err2_1.45.0-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-2 libdpkg-perl_1.19.6 libelf1_0.176-1 libext2fs2_1.45.0-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-7 libgcc-8-dev-armhf-cross_8.3.0-7cross1 libgcc1_1:8.3.0-7 libgcc1-armhf-cross_1:8.3.0-7cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-2 libgomp1_8.3.0-7 libgomp1-armhf-cross_8.3.0-7cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-7 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-7 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-7 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_8.3.0-7 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.0-1 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-armhf-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-armhf-cross_8.3.0-7cross1 libsystemd0_241-3 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libubsan1-armhf-cross_8.3.0-7cross1 libuchardet0_0.0.6-3 libudev1_241-3 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.28-2 linux-libc-dev-armhf-cross_4.19.28-2cross2 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-plink-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 19 06:15:45 2018 UTC gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "bob.dybian@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./plink_1.07+dfsg-2.dsc dpkg-source: info: extracting plink in /<>/plink-1.07+dfsg dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz dpkg-source: info: unpacking plink_1.07+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 30_endiandetection.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying Fix_spelling_error.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-2e08d045-795d-4eca-a82f-2fd2a429f670 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package plink dpkg-buildpackage: info: source version 1.07+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/plink-1.07+dfsg' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>/plink-1.07+dfsg' rm -f *.o *~ make[2]: Leaving directory '/<>/plink-1.07+dfsg' rm -f plink make[1]: Leaving directory '/<>/plink-1.07+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/plink-1.07+dfsg' /usr/bin/make CXXFLAGS='-Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3' FORCE_DYNAMIC=1 make[2]: Entering directory '/<>/plink-1.07+dfsg' g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp In file included from plink.cpp:28: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from plink.cpp:35: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp In file included from options.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp In file included from input.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readData()': input.cpp:516:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i == include.size() ) ~~^~~~~~~~~~~~~~~~~ input.cpp:521:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ input.cpp:545:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ input.cpp:579:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_clst) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:821:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=2; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if ( ccount != tokens.size() ) ~~~~~~~^~~~~~~~~~~~~~~~ input.cpp:965:25: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_pheno) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1037:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (tokens.size() < 2+par::mult_covar) ~~~~~~~~~~~~~~^~~~~~~ input.cpp:1261:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i0=0; i0::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::clist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1519:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] else if (tokens.size() != par::plist_number + 2 ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ input.cpp:1602:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, int&)': input.cpp:2116:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ input.cpp:2225:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ input.cpp: In member function 'void Plink::readFamFile(std::__cxx11::string)': input.cpp:2389:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp In file included from binput.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ binput.cpp: In member function 'void Plink::readBinData()': binput.cpp:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (c<7 && s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp In file included from tinput.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tinput.cpp: In member function 'void Plink::readTransposedData()': tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~ tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int l=0; l < locus.size(); l++) ~~^~~~~~~~~~~~~~ tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( c > sample.size()) ~~^~~~~~~~~~~~~~~ tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * sample.size() ) ~~~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp In file included from genome.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genome.cpp: In member function 'void Plink::calcStratifiedAlleleFreqs()': genome.cpp:99:8: warning: unused variable 'geno_nm' [-Wunused-variable] int geno_nm = 0; ^~~~~~~ genome.cpp:81:14: warning: unused variable 'tothet' [-Wunused-variable] double tothet = 0; ^~~~~~ genome.cpp: In member function 'void Plink::calcFst()': genome.cpp:391:14: warning: unused variable 'ht' [-Wunused-variable] double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq ); ^~ genome.cpp: In member function 'Z Plink::calcGenomeIBD(Individual*, Individual*, Z)': genome.cpp:843:10: warning: unused variable 'e10' [-Wunused-variable] double e10 = E10*S; ^~~ genome.cpp:844:10: warning: unused variable 'e20' [-Wunused-variable] double e20 = E20*S; ^~~ genome.cpp:848:10: warning: unused variable 'e21' [-Wunused-variable] double e21 = E21*S; ^~~ genome.cpp: In member function 'void Plink::displayGenomeWideInfo()': genome.cpp:1067:23: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( (!par::silent ) && c==c2 || c==np) ~~~~~~~~~~~~~~~~^~~~~~~~ genome.cpp: In member function 'void Plink::pruneLD()': genome.cpp:1227:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp In file included from helper.h:24, from helper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string display(std::vector >&)': helper.cpp:58:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&)': helper.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp:79:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In function 'void display(std::vector&)': helper.cpp:100:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< m.size(); i++) ~^~~~~~~~~~ helper.cpp: In member function 'void CArgs::fromPriorLog(std::__cxx11::string)': helper.cpp:193:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int t=0; t > CArgs::value(std::__cxx11::string, int)': helper.cpp:267:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( (i+j) < a.size() ) ~~~~~~^~~~~~~~~~ helper.cpp:277:16: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (r.size() != c) error("Not enough arguments given for option: "+s+" "); ~~~~~~~~~^~~~ helper.cpp: In function 'std::vector > parse2str(std::__cxx11::string)': helper.cpp:306:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0 ; i < s.length() ; i++) ~~^~~~~~~~~~~~ helper.cpp:307:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (s[i] == ',' || i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ helper.cpp:309:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (i == s.length()-1) t += s[i]; ~~^~~~~~~~~~~~~~~ helper.cpp: In function 'std::vector parse2int(std::__cxx11::string)': helper.cpp:323:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i > listPossibleHaplotypes(Plink&, std::vector)': helper.cpp:709:10: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while(h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, matrix_t&, boolmatrix_t&, bool)': helper.cpp:795:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s = 0 ; s < snps.size() ; s++) ~~^~~~~~~~~~~~~ helper.cpp: In function 'std::__cxx11::string chromosomeName(int)': helper.cpp:952:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( c < 0 || c >= par::chr_code.size() ) ~~^~~~~~~~~~~~~~~~~~~~~~~ helper.cpp: In function 'int getMarkerChromosome(Plink&, std::__cxx11::string)': helper.cpp:959:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l getChromosomeMarkerRange(Plink&, int)': helper.cpp:989:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i getChromosomeRange(Plink&)': helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >)': helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->fid.length() > par::pp_maxfid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (sample[i]->iid.length() > par::pp_maxiid) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (locus[l]->name.length() > par::pp_maxsnp) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&)': helper.cpp:2204:12: warning: unused variable 'i' [-Wunused-variable] int i = 0; ^ helper.cpp: In member function 'void Plink::filterOnCovariate()': helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j, Individual*>&)': helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( input.size() != P.nl_all ) ~~~~~~~~~~~~~^~~~~~~~~~~ helper.cpp: In function 'std::map, std::set > readRange(std::__cxx11::string)': helper.cpp:3097:20: warning: unused variable 's' [-Wunused-variable] set * s; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3324:9: warning: unused variable 'last' [-Wunused-variable] int last = -1; ^~~~ helper.cpp:3328:9: warning: unused variable 'thisChromosome' [-Wunused-variable] int thisChromosome = P.locus[0]->chr; ^~~~~~~~~~~~~~ helper.cpp:3329:9: warning: unused variable 'nextChromosome' [-Wunused-variable] int nextChromosome; ^~~~~~~~~~~~~~ helper.cpp: In member function 'std::__cxx11::string CArgs::value(std::__cxx11::string)': helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'int CArgs::value_int(std::__cxx11::string)': helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'long unsigned int CArgs::value_lui(std::__cxx11::string)': helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In member function 'double CArgs::value_double(std::__cxx11::string)': helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type] error("Missing an argument for "+s); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'int getInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:378:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'long unsigned int getLongUnsignedInt(std::__cxx11::string, std::__cxx11::string)': helper.cpp:391:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid integer argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'double getDouble(std::__cxx11::string, std::__cxx11::string)': helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type] error("Not valid numeric argument for : "+a+" [ "+s+" ]"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ helper.cpp: In function 'std::vector vif_prune(std::vector >, double, std::vector&)': helper.cpp:1430:12: warning: 'maxI' may be used uninitialized in this function [-Wmaybe-uninitialized] cur[maxI] = false; ^ helper.cpp: In function 'void makeScaffold(Plink&)': helper.cpp:3342:12: warning: 'ci.CInfo::lstop' may be used uninitialized in this function [-Wmaybe-uninitialized] CInfo ci; ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp In file included from helper.h:24, from stats.cpp:30: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ stats.cpp: In function 'void tqli(std::vector&, std::vector&, std::vector >&)': stats.cpp:458:18: warning: unused variable 'k' [-Wunused-variable] int m,l,iter,i,k; ^ stats.cpp: In function 'bool svd(matrix_t&, vector_t&, matrix_t&)': stats.cpp:813:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^~~ stats.cpp:818:7: warning: unused variable 'r' [-Wunused-variable] int r = u.size(); ^ stats.cpp: In function 'std::vector > msqrt(std::vector >&)': stats.cpp:906:16: warning: unused variable 'eps' [-Wunused-variable] const double eps = 1e-12; ^~~ stats.cpp: In function 'int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)': stats.cpp:1477:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < keep.size(); c++) ~~^~~~~~~~~~~~~ stats.cpp: In function 'matrix_t vec2diag(vector_t&)': stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < v.size(); i++) ~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp In file included from filters.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ filters.cpp: In member function 'void Plink::filterSNPs()': filters.cpp:95:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int l = 0 ; l < locus.size() ; l++ ) ~~^~~~~~~~~~~~~~ filters.cpp:762:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < sample.size() ; i++ ) ~~^~~~~~~~~~~~~~~ filters.cpp:1078:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp In file included from locus.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp In file included from multi.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multi.cpp: In member function 'std::vector Plink::calcMultiPoint(std::vector&, Z, std::ofstream&)': multi.cpp:295:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp In file included from helper.h:24, from cluster.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cluster.cpp: In member function 'void Plink::buildCluster()': cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=1; z<=qt.size(); z++) ~^~~~~~~~~~~ cluster.cpp:452:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:651:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0;k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=i+1; j::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cluster.cpp:1038:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int j=0;j >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true; ~~~~~~~~~^~~~~ cluster.cpp:1049:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j1=0; j1 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j2=0; j2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&, std::vector&, std::vector&)': cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::vector&)': cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >&, std::vector&, std::vector&)': cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ cluster.cpp:1664:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp In file included from mds.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mds.cpp: In member function 'void Plink::generateMDS()': mds.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i1=0; i1::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i2=0; i2::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( elist.size() != par::cluster_mds_dim ) ~~~~~~~~~~~~~^~~~~~ mds.cpp:242:8: warning: unused variable 'flag' [-Wunused-variable] bool flag = svd(D,eigenvalue,eigenvector); ^~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp In file included from output.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ output.cpp: In member function 'void Plink::displayGenomePV()': output.cpp:84:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::iterator loc1 = locus.begin()+m1; ^~~~ output.cpp:403:28: warning: variable 'loc2' set but not used [-Wunused-but-set-variable] vector::iterator loc2 = locus.begin()+m2; ^~~~ output.cpp: In member function 'void Plink::extractExcludeSet(bool)': output.cpp:520:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < setname.size();i++) ~~^~~~~~~~~~~~~~~~ output.cpp:2380:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp In file included from informative.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ informative.cpp: In member function 'int Plink::readInformative()': informative.cpp:80:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 4; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( col_length != tokens.size() ) ~~~~~~~~~~~^~~~~~~~~~~~~~~~ informative.cpp:105:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp In file included from helper.h:24, from assoc.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from assoc.cpp:29: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:741:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:744:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ assoc.cpp:788:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ assoc.cpp: In member function 'std::vector Plink::fullModelAssoc(bool, Perm&)': assoc.cpp:1536:11: warning: unused variable 'best' [-Wunused-variable] int best = 0 ; ^~~~ assoc.cpp: In member function 'std::vector Plink::testAssoc(int&, int&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, Perm&, bool)': assoc.cpp:1108:4: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] if ( pvalue <= par::set_score_p && pvalue >= 0 ) ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp In file included from epi.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ epi.cpp: In member function 'void Plink::calcEpistasis()': epi.cpp:146:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int e=0;e>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp In file included from prephap.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from prephap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (len != tokens.size() - offset ) ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ prephap.cpp:283:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = allele ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ prephap.cpp:412:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] while ( index < tokens.size() ) ~~~~~~^~~~~~~~~~~~~~~ prephap.cpp:416:34: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens[index].size() != len ) ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prephap.cpp:420:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( index == tokens.size() - 1 ) ~~~~~~^~~~~~~~~~~~~~~~~~~~ prephap.cpp:470:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp In file included from phase.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from phase.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': phase.cpp:472:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z, int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( nh != hapmap.size() ) ~~~^~~~~~~~~~~~~~~~ phase.cpp:1238:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < pp[i].size() ; z++ ) ~~^~~~~~~~~~~~~~ phase.cpp: In member function 'void HaploPhase::prunePhase(int)': phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ phase.cpp: In member function 'double HaploPhase::dosage(int, std::set&)': phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < h1.size(); z++) ~~^~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp In file included from trio.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp: In function 'void addPerson(Family*, Individual*)': trio.cpp:91:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::parseTrios()': trio.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:272:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~ trio.cpp:335:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ trio.cpp:342:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp:350:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ trio.cpp: In member function 'void Plink::checkMendel()': trio.cpp:469:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0;f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ trio.cpp:962:6: warning: unused variable 'tmp' [-Wunused-variable] int tmp = deleteIndividuals(indel); ^~~ trio.cpp: In member function 'void Plink::pseudoCaseControl()': trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kpm->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ trio.cpp:1245:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kpp->kids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp In file included from tdt.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'void Plink::perm_testTDT(Perm&)': tdt.cpp:81:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iperson.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:96:16: warning: unused variable 'person' [-Wunused-variable] Individual * person = klist[k]->person[i]; ^~~~~~ tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c < fam->kid.size(); c++) ~~^~~~~~~~~~~~~~~~~ tdt.cpp:210:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; iprofileSNPs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; jselectedSNPs[l].size(); j++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < pS->selectedSNPs[l].size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ tdt.cpp:415:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ tdt.cpp: In member function 'std::vector Plink::testTDT(bool, bool, Perm&, std::vector&, std::vector&)': tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp In file included from perm.h:17, from sharing.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sharing.cpp: In member function 'void Plink::perm_sharingIBSTest(Perm&)': sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp In file included from genepi.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genepi.cpp: In function 'double C(int, double, double)': genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ genepi.cpp: In function 'long double pillai(int, int, int, double)': genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ genepi.cpp: In member function 'void Plink::driverSCREEPI()': genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >&, Set&, Plink&)': genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l >&, Set&, Plink&)': genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l&, int, int, bool, Plink*, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&)': genepi.cpp:1198:8: warning: unused variable 'casewise_deletion' [-Wunused-variable] bool casewise_deletion = false; ^~~~~~~~~~~~~~~~~ genepi.cpp: In function 'void CCA_logit(bool, std::vector >&, Set&, Plink&)': genepi.cpp:805:82: warning: 'cancor1_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j]; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp In file included from sets.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from sets.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int s=0;s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if (par::set_min > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp:62:41: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (par::set_max==-1 || par::set_max > snpset[i].size() ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::pruneSets(Plink&)': sets.cpp:99:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:236:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::makeLDSets()': sets.cpp:317:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:329:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:332:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=j+1; k < snpset[i].size(); k++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp:367:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < snpset[i].size(); j++) ~~^~~~~~~~~~~~~~~~~~ sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp In file included from perm.h:17, from perm.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ perm.cpp: In member function 'void Perm::permuteInCluster()': perm.cpp:144:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i&, std::vector&)': perm.cpp:273:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j< P.pS->snpset[l].size();j++) ~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp In file included from perm.h:17, from mh.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ mh.cpp: In member function 'std::vector Plink::calcMantelHaenszel_IxJxK(std::vector&, std::vector&, std::vector&)': mh.cpp:747:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i Plink::calcMantelHaenszel_ORD(std::vector&, std::vector&, std::vector&)': mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp In file included from perm.h:17, from genedrop.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ genedrop.cpp: In member function 'void Perm::preGeneDrop()': genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, std::vector&, std::vector&, std::map&)': genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; kkids.size(); k++) ~^~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp In file included from helper.h:24, from gxe.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp In file included from merge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ merge.cpp: In member function 'void Plink::mergeData()': merge.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i > include.size()) ~~^~~~~~~~~~~~~~~~ merge.cpp:733:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( gn != 2 * include.size() ) ~~~^~~~~~~~~~~~~~~~~~~~~ merge.cpp:784:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i, int>&)': merge.cpp:1103:3: warning: 'write' may be used uninitialized in this function [-Wmaybe-uninitialized] if (write) ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp In file included from hotel.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ hotel.cpp: In member function 'void Plink::perm_testHotel(Perm&)': hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (!sample[i]->missing) ^ hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp In file included from helper.h:24, from multiple.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ multiple.cpp: In member function 'void Plink::multcomp(std::vector&, std::__cxx11::string)': multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp In file included from haploCC.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploCC.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:62:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:79:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:93:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:268:14: warning: unused variable 'p' [-Wunused-variable] double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 ); ^ haploCC.cpp: In member function 'void HaploPhase::haplotypicWeightedCC()': haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:357:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ haploCC.cpp:375:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploCC.cpp:392:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if ( ! ( haploid || X && person->sex ) ) ~~^~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp In file included from haploTDT.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploTDT.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp In file included from poo.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'void Plink::perm_testTDT_POO(Perm&)': poo.cpp:93:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ipv_set.size();i++) ~^~~~~~~~~~~~~~~~~~ poo.cpp:198:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;jpv_set[i].size();j++) ~^~~~~~~~~~~~~~~~~~~~~ poo.cpp: In member function 'std::vector Plink::testTDT_POO(bool, bool, Perm&, std::vector&, std::vector&)': poo.cpp:293:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp In file included from helper.h:24, from webcheck.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ webcheck.cpp: In member function 'void Plink::webcheck(CArgs&)': webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:146:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size()-1 ) ~~^~~~~~~~~~~~~~~~~ webcheck.cpp:180:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( i < tokens.size() - 1) ~~^~~~~~~~~~~~~~~~~~~ webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp In file included from helper.h:24, from qfam.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp: In function 'void scoreBetween(Plink&, int)': qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k < (*f)->kid.size() ;k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:89:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp:97:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; k<(*f)->kid.size(); k++) ~^~~~~~~~~~~~~~~~~ qfam.cpp: In member function 'void Plink::perm_testQTDT(Perm&)': qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < family.size(); i++) ~~^~~~~~~~~~~~~~~ qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < family.size() ; f++) ~~^~~~~~~~~~~~~~~ qfam.cpp: In member function 'vector_t Plink::calcQTDT(std::vector&, std::ofstream&, bool, Perm&, std::vector&, std::vector&)': qfam.cpp:505:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < (*f)->kid.size() ; k++) ~~^~~~~~~~~~~~~~~~~~ qfam.cpp:648:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp In file included from helper.h:24, from linear.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linear.cpp: In member function 'virtual void LinearModel::pruneY()': linear.cpp:50:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp In file included from bmerge.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ bmerge.cpp: In member function 'void Plink::mergeBinaryData()': bmerge.cpp:90:16: warning: variable 'inc' set but not used [-Wunused-but-set-variable] long int inc; ^~~ bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~~~ bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] while (s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp In file included from parse.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ parse.cpp: In function 'void setOptions(CArgs&)': parse.cpp:80:6: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without void setOptions(CArgs & a) ^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp In file included from mishap.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from mishap.cpp:20: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:236:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:349:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ mishap.cpp:373:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < haplo->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp In file included from helper.h:24, from legacy.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ legacy.cpp: In member function 'void Plink::calcRegression(int)': legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp In file included from helper.h:24, from homozyg.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ homozyg.cpp: In function 'void displayPoolVerbose(Plink&, Pool*, std::ofstream&)': homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp:861:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < plist.size(); i++) ~~^~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::summariseHomoRuns()': homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1178:31: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( thispool->segs.size() >= par::pool_size_min ) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::set >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< (*pA)->segs.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1437:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp:1441:33: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( (*pA)->match[i].size() >= maxlist ) ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ homozyg.cpp:1461:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < (*pA)->group.size() ; i++) ~~^~~~~~~~~~~~~~~~~~~~~ homozyg.cpp: In member function 'void Plink::findHomoWindow(Individual*, std::ofstream&)': homozyg.cpp:2155:20: warning: value computed is not used [-Wunused-value] homozygWindows[l] == 0; g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp In file included from helper.h:24, from segment.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ segment.cpp: In member function 'void Plink::segmentPermutationTest(Perm&, bool, std::__cxx11::string, std::vector&, std::vector&, std::vector&)': segment.cpp:871:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!ibd) ^~ segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' SIBS << setw(10) << original[l] << " " ^~~~ segment.cpp: In member function 'void Plink::testGenomeIBDByCovariate(Perm&)': segment.cpp:954:15: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:955:15: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:1027:19: warning: unused variable 'p1' [-Wunused-variable] Individual * p1 = sample[i1]; ^~ segment.cpp:1028:19: warning: unused variable 'p2' [-Wunused-variable] Individual * p2 = sample[i2]; ^~ segment.cpp:950:7: warning: unused variable 'c' [-Wunused-variable] int c=0; ^ segment.cpp: In member function 'void Plink::summaryIBD()': segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0;ifirst; ^ segment.cpp: In member function 'void Plink::displaySegmentsLong()': segment.cpp:2003:12: warning: unused variable 'nseg' [-Wunused-variable] int nseg = smap.size(); ^~~~ segment.cpp: In member function 'void Plink::displaySegmentsBED()': segment.cpp:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 1 ) ~~~~~~~~~~~~~^~~ segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 2 ) ~~~~~~~~~~~~~^~~ segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses] else if ( par::cnv_col = 3 ) ~~~~~~~~~~~~~^~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp In file included from model.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from model.cpp:17: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&)': model.cpp:132:23: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( include.size() != P->n ) ~~~~~~~~~~~~~~~^~~~~~~ model.cpp: In member function 'void Model::buildDesignMatrix()': model.cpp:354:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< par::parameter_list.size(); i++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:367:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < X.size() ; i++) ~~^~~~~~~~~~ model.cpp:374:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < par::parameter_list.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'bool Model::checkVIF()': model.cpp:613:10: warning: unused variable 'maxVIF' [-Wunused-variable] double maxVIF = 0; ^~~~~~ model.cpp: In member function 'double Model::buildQFAM(Individual*)': model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type] error("Internal problem with QFAM model specification"); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp In file included from helper.h:24, from logistic.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ logistic.cpp: In member function 'virtual void LogisticModel::pruneY()': logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp In file included from helper.h:24, from glm.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from glm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=1; h < whap->current->group.size(); h++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glm.cpp:344:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp dcdflib.cpp: In function 'void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:1882:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.cpp: In function 'void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)': dcdflib.cpp:3544:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp: In function 'void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)': dcdflib.cpp:6025:60: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp:6088:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~~~~~^~~~~~~~~~~~~ dcdflib.cpp:6112:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6153:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ dcdflib.cpp:6020:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable] static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup; ^~~ dcdflib.cpp: In function 'double dlanor(double*)': dcdflib.cpp:6401:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp: In function 'double dstrem(double*)': dcdflib.cpp:6782:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ dcdflib.cpp: In function 'void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)': dcdflib.cpp:6996:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp In file included from helper.h:24, from elf.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In function 'void displayScoresRegion(std::ofstream&, RCount&)': elf.cpp:493:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ elf.cpp: In member function 'void Plink::permTestRareDistribution(Perm&)': elf.cpp:609:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< original.size(); l++) ~^~~~~~~~~~~~~~~~~ elf.cpp: In member function 'vector_t Plink::testRareDistribution(Perm&, bool, std::map&)': elf.cpp:654:16: warning: unused variable 'pthresh' [-Wunused-variable] const double pthresh = 0.01; ^~~~~~~ elf.cpp:655:8: warning: unused variable 'one_sided' [-Wunused-variable] bool one_sided = true; ^~~~~~~~~ elf.cpp:707:7: warning: unused variable 'srange_cnt' [-Wunused-variable] int srange_cnt = 0; ^~~~~~~~~~ elf.cpp:708:8: warning: unused variable 'inRange' [-Wunused-variable] bool inRange = false; ^~~~~~~ elf.cpp: In member function 'void Plink::displayRareRange()': elf.cpp:895:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++) ~~^~~~~~~~~~~~~~~ elf.cpp:939:26: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != ncol ) ~~~~~~~~~~~~~~^~~~~~~ elf.cpp: In member function 'bool RCount::addSNP(int)': elf.cpp:374:10: warning: 'wt' may be used uninitialized in this function [-Wmaybe-uninitialized] double wt; ^~ elf.cpp: In member function 'void Plink::elfBaseline()': elf.cpp:1154:8: warning: 'p_gcnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_gcnt); ^~~~~~~~~~~ elf.cpp:1165:5: warning: 'p_cnt' may be used uninitialized in this function [-Wmaybe-uninitialized] ++(*p_cnt); ^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp In file included from dfam.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ dfam.cpp: In member function 'std::vector Plink::testSibTDT(bool, bool, Perm&, std::vector&, std::vector&)': dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k=0; kkid.size(); k++) ~^~~~~~~~~~~~~~~~ dfam.cpp:106:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:378:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; ckid.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:218:9: warning: unused variable 'informative' [-Wunused-variable] bool informative = false; ^~~~~~~~~~~ dfam.cpp:504:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; cperson.size(); c++) ~^~~~~~~~~~~~~~~~~~~~~~~~ dfam.cpp:151:11: warning: unused variable 'totalInformative' [-Wunused-variable] int totalInformative = 0; ^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp In file included from helper.h:24, from fisher.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ fisher.cpp: In function 'void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)': fisher.cpp:261:61: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:267:55: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:273:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp: In function 'void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)': fisher.cpp:448:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(1, "NROW must be less than or equal to LDTABL."); ^ fisher.cpp:450:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(4, "NCOL must be at least 2"); ^ fisher.cpp:449:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (*ncol <= 1) ^~ fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' for (i = 1; i <= *ldkey << 1; ++i) { ^~~ fisher.cpp:501:59: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(2, "All elements of TABLE must be positive."); ^ fisher.cpp:509:54: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "PRT and PRE are set to missing values."); ^ fisher.cpp:563:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Reduce the workspace size, or use `exact = FALSE'."); ^ fisher.cpp:751:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)': fisher.cpp:1539:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1555:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp:1597:57: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] "Try increasing the size of the workspace."); ^ fisher.cpp: In function 'int iwork(int, int*, int, int)': fisher.cpp:2001:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(40, "Out of workspace."); ^ fisher.cpp: In function 'void isort(int*, int*)': fisher.cpp:2078:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] prterr(20, "This should never occur."); ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp In file included from linput.cpp:25: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ linput.cpp: In member function 'void Plink::readDataLongFormat()': linput.cpp:68:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:128:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< locus.size(); l++) ~^~~~~~~~~~~~~~ linput.cpp:164:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp In file included from helper.h:24, from sockets.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ sockets.cpp: In function 'std::vector > socketConnection(Plink*, std::__cxx11::string, int, std::__cxx11::string)': sockets.cpp:78:24: warning: unused variable 'out_buf' [-Wunused-variable] char out_buf[BUF_SIZE+1]; // Output buffer for GET request ^~~~~~~ sockets.cpp:79:24: warning: unused variable 'in_buf' [-Wunused-variable] char in_buf[BUF_SIZE+1]; // Input buffer for response ^~~~~~ sockets.cpp:81:24: warning: unused variable 'i' [-Wunused-variable] unsigned int i; // Loop counter ^ sockets.cpp:119:7: warning: unused variable 'echoStringLen' [-Wunused-variable] int echoStringLen = 100; ^~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp In file included from helper.h:24, from lookup.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup.cpp: In member function 'void Plink::lookup()': lookup.cpp:206:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=25; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp In file included from proxy.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from proxy.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=1; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( added.size() >= par::proxy_snp_filter ) ~~~~~~~~~~~~~^~~~~~ proxy.cpp:854:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1332:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c1 = 0; c1 < collection.size() ; c1++ ) ~~~^~~~~~~~~~~~~~~~~~~ proxy.cpp:1448:12: warning: unused variable 't1' [-Wunused-variable] int t1=0; ^~ proxy.cpp:169:10: warning: unused variable 's' [-Wunused-variable] CSNP * s = SNP[l]; ^ proxy.cpp:939:58: warning: 'ref' may be used uninitialized in this function [-Wmaybe-uninitialized] haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " "; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp In file included from pdriver.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from pdriver.cpp:18: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp In file included from haploQTL.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haploQTL.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i&, int, bool)': haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haploQTL.cpp:145:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0 ; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp In file included from haplohelper.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplohelper.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l < actual_map.size(); l++) ~~^~~~~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'std::vector > HaploPhase::returnHaplotypes(std::vector&)': haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp:413:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplohelper.cpp: In member function 'vector_t HaploPhase::imputeGenotype(int, int)': haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] ||alleles2.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'double HaploPhase::freq(boolvec_t&, boolvec_t&)': haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~^~~~~ haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (mask1.size() != ns ||alleles1.size() != ns ) ~~~~~~~~~~~~~~~~^~~~~ haplohelper.cpp: In member function 'void HaploPhase::trackThisSegment()': haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[p1].size(); z++) ~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z1 = 0; z1 < hap1[p1].size(); z1++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2 = 0; z2 < hap1[p2].size(); z2++) ~~~^~~~~~~~~~~~~~~~~ haplohelper.cpp:1250:11: warning: unused variable 'j' [-Wunused-variable] int j=0; ^ haplohelper.cpp: In member function 'void HaploPhase::calculateEmpiricalVariance(std::set&)': haplohelper.cpp:1419:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp:1477:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int z = 0; z < pp[i].size(); z++ ) ~~^~~~~~~~~~~~~~ haplohelper.cpp: In member function 'void HaploPhase::verboseDisplayWindows(int, bool)': haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < windows[w]->hap1[r].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp In file included from haplowindow.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from haplowindow.cpp:27: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::enumerateHaplotypes(intvec_t&)': haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < new_pp.size(); z++) ~~^~~~~~~~~~~~~~~ haplowindow.cpp: In member function 'void HaploWindow::performEM()': haplowindow.cpp:683:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ haplowindow.cpp:966:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp In file included from genogroup.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genogroup.cpp:24: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp In file included from nonfounderphasing.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from nonfounderphasing.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z < pp[i].size(); z++) ~~^~~~~~~~~~~~~~ nonfounderphasing.cpp:360:7: warning: unused variable 'pcnt' [-Wunused-variable] int pcnt=1; ^~~~ nonfounderphasing.cpp: In member function 'void HaploPhase::transmissionCount(int, std::map&)': nonfounderphasing.cpp:715:14: warning: unused variable 'posterior' [-Wunused-variable] double posterior = ip->second; ^~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp In file included from helper.h:24, from clumpld.h:21, from clumpld.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from clumpld.cpp:21: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i clump_LD::read_assoc_file(std::__cxx11::string)': clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f=0; f >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clumpld.cpp:174:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clumpld.cpp:201:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( f < annot_field.size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ clumpld.cpp: In member function 'void clump_LD::clump()': clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < sp.size(); i++) ~~^~~~~~~~~~~ clumpld.cpp:480:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( l1 < P->locus.size()-1 ) ~~~^~~~~~~~~~~~~~~~~~~ clumpld.cpp:520:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:611:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=1; f<=filename.size(); f++) ~^~~~~~~~~~~~~~~~~ clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] if( j < grouped_snps.size()-1) ~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp In file included from genoerr.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from genoerr.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int a = 0; a < posshap1.size(); a++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:190:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for( int b = 0; b < posshap2.size(); b++ ) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~ genoerr.cpp:328:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z = 0; z < new_hap1.size(); z++) ~~^~~~~~~~~~~~~~~~~ genoerr.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z2=0; z2>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp In file included from em.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from em.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp In file included from impute.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from impute.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->hap1[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:161:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z< currentWindow->pp[i].size(); z++) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp: In member function 'void HaploPhase::mainImputation()': impute.cpp:263:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ impute.cpp:313:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s < g.size(); s++) ~~^~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp In file included from metaem.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from metaem.cpp:27: genogroup.h: In member function 'bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const': genogroup.h:27:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp In file included from profile.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::scoreIndividuals()': profile.cpp:303:12: warning: unused variable 'OLD_assoc_glm_without_main_snp' [-Wunused-variable] bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ profile.cpp:304:12: warning: unused variable 'OLD_clist' [-Wunused-variable] bool OLD_clist = par::clist; ^~~~~~~~~ profile.cpp:350:14: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ profile.cpp:351:14: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ profile.cpp:352:14: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ profile.cpp:390:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( qcnt == qlabel.size() ) ~~~~~^~~~~~~~~~~~~~~~ profile.cpp: In member function 'void Plink::calculateProfile(std::map&, std::map&, vector_t&, matrix_t&, std::vector&, std::vector&)': profile.cpp:480:9: warning: unused variable 'a1' [-Wunused-variable] bool a1 = i2->second; ^~ profile.cpp:525:9: warning: variable 'sawNamedAllele' set but not used [-Wunused-but-set-variable] bool sawNamedAllele = false; ^~~~~~~~~~~~~~ profile.cpp:629:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j&, std::map >&, std::map&, std::ofstream&)': profile.cpp:667:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp In file included from helper.h:24, from nlist.h:21, from nlist.cpp:17: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ nlist.cpp: In member function 'std::vector NList::deparseNumberList(std::__cxx11::string)': nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i NList::deparseStringList(std::__cxx11::string, std::map, int>*)': nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i NList::expandNumberList(std::vector&)': nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i > NList::tokenize(std::__cxx11::string)': nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( s[i]== range_char && i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] else if ( i == s.length()-1 ) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp In file included from helper.h:24, from whap.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from whap.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g = 0; g < nullModel.group.size(); g++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:393:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; g::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g=0; g >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g2=0; g2 >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( g < nullModel.group.size() - 1 ) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:670:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s < conditioner.size(); s++) ~~^~~~~~~~~~~~~~~~~~~~ whap.cpp:793:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp:793:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p1 != coeff1.size() || p0 != coeff0.size() ) ~~~^~~~~~~~~~~~~~~~ whap.cpp: In member function 'void Chap::build(ChapModel&)': whap.cpp:962:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< tok.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < tok.size() ; i++ ) ~~^~~~~~~~~~~~ whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: 'std::map, int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( mapping.size() != H->ns + H->nh ) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i< lst.size(); i++) ~^~~~~~~~~~~~ whap.cpp:1142:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; g< model.group.size(); g++) ~^~~~~~~~~~~~~~~~~~~~ whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c=0; c < P->conditioner.size(); c++) ~~^~~~~~~~~~~~~~~~~~~~~~~ whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l&, ChapModel&)': whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0;l >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int h=0; h < m.group.size(); h++) ~~^~~~~~~~~~~~~~~~ whap.cpp:1434:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::set::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( cnt>0 && cnt2 < m.group[h].size() ) ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp In file included from helper.h:24, from simul.cpp:16: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ simul.cpp: In function 'vector_t instanceSNP(SimParameters&)': simul.cpp:172:10: warning: unused variable 'gh_11_12' [-Wunused-variable] double gh_11_12 = h11*h12; ^~~~~~~~ simul.cpp: In member function 'void Plink::simulateSNPs()': simul.cpp:635:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp In file included from helper.h:24, from gvar.cpp:15: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ gvar.cpp: In member function 'void Plink::readGenericVariantData()': gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; isecond; ^~ gvar.cpp:414:8: warning: unused variable 'fatal' [-Wunused-variable] bool fatal = false; ^~~~~ gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp In file included from helper.h:24, from cnv.cpp:23: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'void Plink::readCNVList()': cnv.cpp:247:8: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:247:11: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:12: warning: unused variable 'p1' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:332:15: warning: unused variable 'p2' [-Wunused-variable] int p1,p2; ^~ cnv.cpp:678:36: warning: variable 'is' set but not used [-Wunused-but-set-variable] map::iterator is = idescription.find(*ir); ^~ cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s1=0; s1::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s2=s1+1; s2::iterator i2 = isection.begin(); ^~ cnv.cpp:1103:36: warning: variable 'il' set but not used [-Wunused-but-set-variable] map::iterator il = segmentLength.find(t); ^~ cnv.cpp:1414:11: warning: unused variable 'nseg' [-Wunused-variable] int nseg = 1; ^~~~ cnv.cpp:412:7: warning: unused variable 'nseg' [-Wunused-variable] int nseg=0; ^~~~ cnv.cpp: In function 'double weighted_count_intersects(std::set&, int, int, int)': cnv.cpp:1749:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ cnv.cpp: In member function 'void Plink::positionPermuteSegments()': cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::map::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int c = 0 ; c < scaffold.size(); c++) ~~^~~~~~~~~~~~~~~~~ cnv.cpp: In member function 'vector_t Plink::glmCNVBurdenModel(Perm&, bool)': cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value] noCovar == true; ~~~~~~~~^~~~~~~ cnv.cpp:2202:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] indivPair p = ic->first; ^ cnv.cpp:2288:10: warning: unused variable 'statistic' [-Wunused-variable] double statistic = valid ? model->getStatistic() : 0; ^~~~~~~~~ cnv.cpp:2289:10: warning: unused variable 'pvalue' [-Wunused-variable] double pvalue = pval[ pval.size()-1 ]; ^~~~~~ cnv.cpp:2290:10: warning: unused variable 'beta' [-Wunused-variable] double beta = b[ b.size()-1 ]; ^~~~ cnv.cpp: In member function 'void Plink::processCNVList()': cnv.cpp:1500:13: warning: 'cdet.CInfo::lstart' may be used uninitialized in this function [-Wmaybe-uninitialized] CInfo cdet; ^~~~ cnv.cpp:1500:13: warning: 'cdet.CInfo::lstop' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp In file included from helper.h:24, from step.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp In file included from greport.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ greport.cpp: In member function 'void Plink::displayGeneReport()': greport.cpp:78:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:148:19: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ greport.cpp:156:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ greport.cpp:169:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ greport.cpp:240:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int l=0; l< ari->second.size(); l+=2) ~^~~~~~~~~~~~~~~~~~~~ greport.cpp:125:7: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp In file included from helper.h:24, from flip.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp In file included from helper.h:24, from qualscores.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ qualscores.cpp: In member function 'void Plink::filterQualGenotypes()': qualscores.cpp:122:12: warning: unused variable 'nfound' [-Wunused-variable] long int nfound = 0; ^~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp In file included from helper.h:24, from cnvqt.cpp:22: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp In file included from cfamily.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ cfamily.cpp: In function 'int mCount(Individual*, Individual*)': cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:221:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp: In function 'bool isAncestorOf(Individual*, Individual*)': cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < inds[i]->kids.size() ; j++) ~~^~~~~~~~~~~~~~~~~~~~~~ cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < inds.size() ; i++) ~~^~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp In file included from setscreen.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ setscreen.cpp: In member function 'void Plink::setAssocSummary()': setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != cols ) ~~~~~~~~~~~~~~^~~~~~~ setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < pS->snpset.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i < snpset[j].size(); i++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp In file included from idhelp.cpp:18: idhelp.h: In member function 'void IDGroup::display()': idhelp.h:196:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'std::map > IDHelper::parseQuery(std::__cxx11::string)': idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:63:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >&)': idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int g=0; gvalues.size(); g++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::map >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( found != matchTemplate.size() ) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:128:8: warning: unused variable 'match' [-Wunused-variable] bool match = true; ^~~~~ idhelp.cpp: In member function 'void IDHelper::setJointValues(IDGroup*)': idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:296:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i = 0 ; i < mask.size() ; i++) ~~^~~~~~~~~~~~~ idhelp.cpp:214:26: warning: unused variable 'jo' [-Wunused-variable] vector & jo = jointOrder[j]; ^~ idhelp.cpp: In member function 'std::set IDHelper::findAllIndividuals(std::map >&)': idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idHelp()': idhelp.cpp:502:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( p < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:542:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:547:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:553:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:529:10: warning: unused variable 'seenJoint' [-Wunused-variable] bool seenJoint = true; ^~~~~~~~~ idhelp.cpp:584:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:594:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size() ; i++) ~~^~~~~~~~~~~~ idhelp.cpp:678:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++p == tokens.size() ) ~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:747:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:757:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:744:23: warning: unused variable 'jf' [-Wunused-variable] set & jf = jointField[j]; ^~ idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < jointField.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int f = 0 ; f < files.size() ; f++ ) ~~^~~~~~~~~~~~~~ idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:836:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ idhelp.cpp:888:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != file->uniqFieldCount ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:894:31: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] int mx = tokens.size() > file->uniqFieldCount ? tokens.size() : file->uniqFieldCount ; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:903:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( j < tokens.size() ) ~~^~~~~~~~~~~~~~~ idhelp.cpp:922:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0 ; j < files[f].fields.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:950:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( v->value.size() + 3 > myField->width ) ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1015:17: warning: unused variable 'group' [-Wunused-variable] IDGroup * group = idgroup[g]; ^~~~~ idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1031:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1085:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1110:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1128:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0; k < (*i0)->values.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1183:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; zvalues.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1189:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int z=0; z<(*i0)->values.size(); z++) ~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1245:14: warning: unused variable 'v' [-Wunused-variable] IDValue & v = *(group->values[j]); ^ idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int j = 0; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idReplace()': idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < targetFields.size(); f++) ~~^~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1649:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size(); i++) ~~^~~~~~~~~~~~~~~ idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= maxfield ) ~~~~~~~~~~~~~~^~~~~~~~~~~ idhelp.cpp:1692:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < thisGroup->values.size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1770:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < tokens.size() ; i++ ) ~~^~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idMatch()': idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int s=0; s< par::idhelp_match_string.size(); s+=2) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idhelp.cpp:1903:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < fieldNames.size(); f++) ~~^~~~~~~~~~~~~~~~~~~ idhelp.cpp:2018:22: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != tableSize[t] ) idhelp.cpp:2024:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( maxF >= tok.size() ) ~~~~~^~~~~~~~~~~~~ idhelp.cpp:2034:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int v=0; vvalues.size(); v++) ~^~~~~~~~~~~~~~~~~ idhelp.cpp:1889:12: warning: unused variable 'jointQuery' [-Wunused-variable] bool jointQuery = id.find("+") != string::npos; ^~~~~~~~~~ idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k = 0 ; k < thisLine.size() ; k++ ) ~~^~~~~~~~~~~~~~~~~ idhelp.cpp: In member function 'void IDHelper::idDump()': idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int g = 0 ; g < idgroup.size(); g++ ) ~~^~~~~~~~~~~~~~~~ idhelp.cpp:2234:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0 ; j < group->values.size(); j++ ) ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp In file included from helper.h:24, from tag.cpp:24: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp In file included from helper.h:24, from hapglm.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from hapglm.cpp:25: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp In file included from helper.h:24, from lookup2.cpp:18: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ lookup2.cpp: In member function 'void Plink::lookup2()': lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0 ; i < ids.size(); i++) ~~^~~~~~~~~~~~ lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int t = 0 ; t < tokens.size() ; t++) ~~^~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp In file included from blox.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from blox.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i > Plink::mkBlks(int, int)': blox.cpp:147:11: warning: unused variable 'nsnps' [-Wunused-variable] int nsnps = toPosition - fromPosition + 1; ^~~~~ blox.cpp:156:11: warning: unused variable 'numStrong' [-Wunused-variable] int numStrong = 0; ^~~~~~~~~ blox.cpp:157:11: warning: unused variable 'numRec' [-Wunused-variable] int numRec = 0; ^~~~~~ blox.cpp:158:11: warning: unused variable 'numInGroup' [-Wunused-variable] int numInGroup = 0; ^~~~~~~~~~ blox.cpp:226:11: warning: unused variable 'cnt' [-Wunused-variable] int cnt = 0; ^~~ blox.cpp:418:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int k=0; k0 ) loglike1 += knownBA * log( pB1 ); ~~~^~~~~~~ blox.cpp:505:10: warning: 'pB1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ blox.cpp:503:10: warning: 'pA2' may be used uninitialized in this function [-Wmaybe-uninitialized] double pA = pA1 + pA2; ^~ blox.cpp:505:10: warning: 'pA1' may be used uninitialized in this function [-Wmaybe-uninitialized] double p1 = pA1 + pB1; ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp In file included from helper.h:24, from zed.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp In file included from dosage.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from dosage.cpp:23: phase.h: In member function 'void HaploPhase::reset()': phase.h:252:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int q = 0 ; q < qthresh.size() ; q++) ~~^~~~~~~~~~~~~~~~ dosage.cpp:513:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < vzin.size() ; f++ ) ~~^~~~~~~~~~~~~ dosage.cpp:581:20: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tok.size() < firstCol ) ~~~~~~~~~~~^~~~~~~~~~ dosage.cpp:601:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=firstCol; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < personMap[f].size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~ dosage.cpp:750:24: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] if ( tok.size() != expected[f] ) dosage.cpp:989:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int q=0; qgetStatistic() : 0; ^~~~~~~~~ dosage.cpp:1252:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( o->second != dosageFilename_all.size() ) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dosage.cpp:1310:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if ( ++qq == qthresh.size() ) ~~~~~^~~~~~~~~~~~~~~~~ dosage.cpp:190:7: warning: unused variable 'geno_field' [-Wunused-variable] int geno_field = a2_field + skip2 + 1; ^~~~~~~~~~ dosage.cpp:915:21: warning: 'snp_code' may be used uninitialized in this function [-Wmaybe-uninitialized] SNP[snp_code]->one[personPosition[f][i]] = s1; ^ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp In file included from annot.cpp:20: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ annot.cpp: In member function 'void Plink::annotateFile()': annot.cpp:83:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j=1; j >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= chr_column || ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:251:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] tokens.size() <= bp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~ annot.cpp:260:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= pval_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ annot.cpp:275:23: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() <= snp_column ) ~~~~~~~~~~~~~~^~~~~~~~~~~~~ annot.cpp:300:9: warning: unused variable 'include' [-Wunused-variable] bool include = false; ^~~~~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp In file included from metaanal.cpp:21: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ metaanal.cpp: In constructor 'Alleles::Alleles(std::__cxx11::string, int, int, std::__cxx11::string, std::__cxx11::string)': metaanal.cpp:47:7: warning: 'Alleles::bp' will be initialized after [-Wreorder] int bp; ^~ metaanal.cpp:44:10: warning: 'std::__cxx11::string Alleles::a1' [-Wreorder] string a1; ^~ metaanal.cpp:61:3: warning: when initialized here [-Wreorder] Alleles(string name, int chr, int bp, string a1, string a2) ^~~~~~~ metaanal.cpp: In member function 'void Plink::metaAnalysis()': metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f = 0 ; f < par::meta_files.size() ; f++ ) ~~^~~~~~~~~~~~~~~~~~~~~~~~ metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i=0; i >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if ( tokens.size() != fsize ) ~~~~~~~~~~~~~~^~~~~~~~ metaanal.cpp:253:11: warning: variable 'pval_column' set but not used [-Wunused-but-set-variable] int pval_column = -1; ^~~~~~~~~~~ metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int f=0; f>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp In file included from helper.h:24, from r.cpp:19: options.h: In member function 'void OptionSet::display()': options.h:73:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for ( int k = 0 ; k < i->second.size(); k++) ~~^~~~~~~~~~~~~~~~~~ In file included from r.cpp:29: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ r.cpp: In member function 'void Plink::Rfunc()': r.cpp:330:8: warning: unused variable 'ct' [-Wunused-variable] int ct = data->length(); ^~ r.cpp:380:9: warning: 'rCov' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rCov; ^~~~ r.cpp:378:14: warning: 'rS' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rS; ^~ r.cpp:377:14: warning: 'rP' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rP; ^~ r.cpp:376:14: warning: 'rN' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rN; ^~ r.cpp:399:10: warning: 'rc' may be used uninitialized in this function [-Wmaybe-uninitialized] delete rc; ^~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp In file included from Rconnection.cpp:30: Rconnection.h: In constructor 'Rsymbol::Rsymbol(Rmessage*)': Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In constructor 'Rsymbol::Rsymbol(unsigned int*, Rmessage*)': Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] { name=""; fix_content(); } ^~ Rconnection.h: In member function 'char* Rstrings::stringAt(int)': Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; } ~^~~~~ Rconnection.h: In member function 'void Rstrings::decode()': Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: 'int' and 'Rsize_t' {aka 'unsigned int'} [-Wsign-compare] while (i < len) { if (!c[i]) nel++; i++; } ~~^~~~~ Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] while (i < nel) { ~~^~~~~ Rconnection.cpp: At global scope: Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */ ^~~~~~~~~~~~~~ Rconnection.cpp: In destructor 'virtual Rconnection::~Rconnection()': Rconnection.cpp:567:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (host) free(host); host=0; ^~ Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (host) free(host); host=0; ^~~~ g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp g++ -Wall -g -fdebug-prefix-map=/<>/plink-1.07+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz /usr/bin/ld: cannot find -lz collect2: error: ld returned 1 exit status make[2]: *** [Makefile:154: plink] Error 1 make[2]: Leaving directory '/<>/plink-1.07+dfsg' make[1]: *** [debian/rules:24: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/plink-1.07+dfsg' make: *** [debian/rules:17: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-05-05T08:28:06Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 331736 Build-Time: 370 Distribution: unstable Fail-Stage: build Foreign Architectures: armhf Host Architecture: armhf Install-Time: 25 Job: plink_1.07+dfsg-2 Machine Architecture: amd64 Package: plink Package-Time: 405 Source-Version: 1.07+dfsg-2 Space: 331736 Status: attempted Version: 1.07+dfsg-2 -------------------------------------------------------------------------------- Finished at 2019-05-05T08:28:06Z Build needed 00:06:45, 331736k disk space