sbuild (Debian sbuild) 0.78.1 (09 February 2019) on 4be29f1fdf49

+==============================================================================+
| plink 1.07+dfsg-2 (armhf)                    Tue, 02 Jul 2019 13:56:26 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-2
Source Version: 1.07+dfsg-2
Distribution: unstable-amd64-sbuild
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-7a86483d-048b-44cf-bfb3-43120d420a1b' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-nTlTEH/resolver-SnriUh' with '<<RESOLVERDIR>>'

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| Update chroot                                                                |
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Hit:1 http://cdn-fastly.deb.debian.org/debian unstable InRelease
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following package was automatically installed and is no longer required:
  sensible-utils
Use 'apt autoremove' to remove it.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

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| Fetch source files                                                           |
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Local sources
-------------

/home/build/sbuild-setup/repo/pool/main/p/plink/plink_1.07+dfsg-2.dsc exists in /home/build/sbuild-setup/repo/pool/main/p/plink; copying to chroot
I: NOTICE: Log filtering will replace 'build/plink-nTlTEH/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-nTlTEH' with '<<BUILDDIR>>'

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| Install package build dependencies                                           |
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Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 11), zlib1g-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf
Filtered Build-Depends: debhelper (>= 11), zlib1g-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
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Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [489 B]
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Reading package lists...
Reading package lists...

Install main 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 binutils-arm-linux-gnueabihf
  bsdmainutils cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config
  crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf
  gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-base:armhf
  gcc-8-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross
  libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf
  libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libdebian-dpkgcross-perl
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-8-dev:armhf libgcc-8-dev-armhf-cross libgcc1:armhf
  libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf
  libstdc++-8-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libtool
  libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf
  linux-libc-dev-armhf-cross m4 man-db po-debconf ucf zlib1g:armhf
  zlib1g-dev:armhf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
  | wordlist whois vacation gcc-8-locales cpp-doc dh-make 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 flex bison gdb-arm-linux-gnueabihf
  gcc-doc 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 libyaml-shell-perl 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 libwww-perl
  libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf
  bsdmainutils cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config
  crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf
  gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-base:armhf
  gcc-8-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross
  libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf
  libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libdebian-dpkgcross-perl
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-8-dev:armhf libgcc-8-dev-armhf-cross libgcc1:armhf
  libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf
  libstdc++-8-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libtool
  libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf
  linux-libc-dev-armhf-cross m4 man-db po-debconf
  sbuild-build-depends-main-dummy:armhf ucf zlib1g:armhf zlib1g-dev:armhf
0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded.
Need to get 908 B/60.5 MB of archives.
After this operation, 231 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 B]
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Selecting previously unselected package libstdc++-8-dev:armhf.
Preparing to unpack .../79-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 .../80-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 .../81-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-main-dummy:armhf.
Preparing to unpack .../82-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy:armhf (0.invalid.0) ...
Setting up libconfig-inifiles-perl (3.000001-1) ...
Setting up libpipeline1:amd64 (1.5.1-2) ...
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 libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:amd64 (2.58.3-2) ...
No schema files found: doing nothing.
Setting up gcc-8-cross-base (8.3.0-7cross1) ...
Setting up libmagic1:amd64 (1:5.35-4) ...
Setting up linux-libc-dev:armhf (4.19.37-5) ...
Setting up libxml-namespacesupport-perl (1.12-1) ...
Setting up gettext-base (0.19.8.1-9) ...
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 (63.2-2) ...
Setting up libxml-sax-base-perl (1.09-1) ...
Setting up libio-string-perl (1.08-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up cross-config (2.6.15-3) ...
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 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 linux-libc-dev-armhf-cross (4.19.28-2cross2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up ucf (3.0038+nmu1) ...
Setting up dwz (0.12-3) ...
Setting up libuchardet0:amd64 (0.0.6-3) ...
Setting up libfile-homedir-perl (1.004-1) ...
Setting up libbsd0:amd64 (0.9.1-2) ...
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 libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up libtool (2.4.6-10) ...
Setting up libc6-dev-armhf-cross (2.28-10cross2) ...
Setting up m4 (1.4.18-2) ...
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 libstdc++6-armhf-cross (8.3.0-7cross1) ...
Setting up bsdmainutils (11.1.2+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:amd64 (0.6.12-3) ...
Setting up libubsan1-armhf-cross (8.3.0-7cross1) ...
Setting up autoconf (2.69-11) ...
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 groff-base (1.22.4-3) ...
Setting up cpp-arm-linux-gnueabihf (4:8.3.0-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasan5-armhf-cross (8.3.0-7cross1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up libgcc-8-dev-armhf-cross (8.3.0-7cross1) ...
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 po-debconf (1.0.21) ...
Setting up libconfig-auto-perl (0.44-1) ...
Setting up g++-8-arm-linux-gnueabihf (8.3.0-7cross1) ...
Setting up libdebian-dpkgcross-perl (2.6.15-3) ...
Setting up g++-arm-linux-gnueabihf (4:8.3.0-1) ...
Setting up dpkg-cross (2.6.15-3) ...
Setting up crossbuild-essential-armhf (12.6) ...
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-main-dummy:armhf (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10) ...
Processing triggers for ccache (3.7.1-1) ...
Updating symlinks in /usr/lib/ccache ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Initial Foreign Architectures: armhf 
Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.51-3 (2017-12-13) amd64 (x86_64)
Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.7 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_4.19.37-5
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 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_1.0.6-9.1 ccache_3.7.1-1 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_2.6.15-3 crossbuild-essential-armhf_12.6 dash_0.5.10.2-5 debconf_1.5.72 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 dirmngr_2.2.13-2 dose-distcheck_5.0.1-12 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.45.2-1 eatmydata_105-7 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 gnupg_2.2.13-2 gnupg-l10n_2.2.13-2 gnupg-utils_2.2.13-2 gpg_2.2.13-2 gpg-agent_2.2.13-2 gpg-wks-client_2.2.13-2 gpg-wks-server_2.2.13-2 gpgconf_2.2.13-2 gpgsm_2.2.13-2 gpgv_2.2.13-2 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-7 libasan5-armhf-cross_8.3.0-7cross1 libassuan0_2.5.2-1 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_1.0.6-9.1 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 libcap2_1:2.25-2 libcc1-0_8.3.0-7 libcom-err2_1.45.2-1 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_2.6.15-3 libdpkg-perl_1.19.7 libeatmydata1_105-7 libelf1_0.176-1.1 libext2fs2_1.45.2-1 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_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-7 libgomp1-armhf-cross_8.3.0-7cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-7 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3 libldap-common_2.4.47+dfsg-3 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-7 liblua5.2-0_5.2.4-1.1+b2 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 libnpth0_1.6-1 libnspr4_2:4.21-1 libnss3_2:3.44+really3.42.1-2 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 libpopt0_1.16-12 libquadmath0_8.3.0-7 libreadline7_7.0-5 librpm8_4.14.2.1+dfsg1-1 librpmio8_4.14.2.1+dfsg1-1 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 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 libsqlite3-0_3.27.2-3 libss2_1.45.2-1 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_241-5 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_241-5 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_4.19.37-5 linux-libc-dev-armhf-cross_4.19.28-2cross2 login_1:4.5-1.1 lsb-base_10.2019051400 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_2.7.6-4 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 readline-common_7.0-5 sbuild-build-depends-dose3-dummy_0.invalid.0 sbuild-build-depends-main-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
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Andreas Tille <tille@debian.org>, Charles Plessy <plessy@debian.org>, Dylan Aïssi <bob.dybian@gmail.com>
Homepage: http://zzz.bwh.harvard.edu/plink/
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/plink
Vcs-Git: https://salsa.debian.org/med-team/plink.git
Testsuite: autopkgtest
Build-Depends: debhelper (>= 11), zlib1g-dev
Package-List:
 plink deb science optional arch=any
Checksums-Sha1:
 c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz
 85431ffbe6da01ff7e8ed44136609f6a38d30f21 16688 plink_1.07+dfsg-2.debian.tar.xz
Checksums-Sha256:
 e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz
 061655d668294a208f8425e77590f6a33b6069417b0d6af4b884e2a4e80c4481 16688 plink_1.07+dfsg-2.debian.tar.xz
Files:
 fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz
 a9275e2b311a137b8f34da00af3e5ecc 16688 plink_1.07+dfsg-2.debian.tar.xz

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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 /<<PKGBUILDDIR>>
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
CCACHE_COMPRESS=1
CCACHE_DIR=/var/cache/ccache-sbuild
CCACHE_UMASK=002
CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
LOGNAME=build
PATH=/usr/lib/ccache:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=build
SCHROOT_SESSION_ID=unstable-amd64-sbuild-7a86483d-048b-44cf-bfb3-43120d420a1b
SCHROOT_UID=1000
SCHROOT_USER=build
SHELL=/bin/sh
USER=build

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot -j16
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 <bob.dybian@gmail.com>
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 '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j16 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o *~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f plink
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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 '/<<PKGBUILDDIR>>'
/usr/bin/make CXXFLAGS='-Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>'
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
multi.cpp: In member function ‘std::vector<double> Plink::calcMultiPoint(std::vector<Z>&, Z, std::ofstream&)’:
multi.cpp:295:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<left.size();i++)
                    ~^~~~~~~~~~~~
multi.cpp:304:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<left.size();i++)
                    ~^~~~~~~~~~~~
multi.cpp:357:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0;i<right.size();i++)
                     ~^~~~~~~~~~~~~
multi.cpp:372:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<pos.size()-1; i++)
                  ~^~~~~~~~~~~~~
multi.cpp:154:8: warning: unused variable ‘is0zero’ [-Wunused-variable]
   bool is0zero = IBDg.z0 < EPS ? true : false;
        ^~~~~~~
multi.cpp:155:8: warning: unused variable ‘is1zero’ [-Wunused-variable]
   bool is1zero = IBDg.z1 < EPS ? true : false;
        ^~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i1=0; i1<cl[c1].size(); i1++)
                  ~~^~~~~~~~~~~~~~
mds.cpp:191:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i2=0; i2<cl[c2].size(); i2++)
                    ~~^~~~~~~~~~~~~~
mds.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for ( int i = 4; i<tokens.size(); i++)
                    ~^~~~~~~~~~~~~~
informative.cpp:102:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<tokens.size();i++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int e=0;e<snpset[0].size();e++)
                    ~^~~~~~~~~~~~~~~~~
epi.cpp:154:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int e=0;e<snpset[1].size();e++)
                 ~^~~~~~~~~~~~~~~~~
epi.cpp:161:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int e=0;e<snpset[0].size();e++)
                 ~^~~~~~~~~~~~~~~~~
epi.cpp:438:12: warning: unused variable ‘zero’ [-Wunused-variable]
     double zero = 0;
            ^~~~
epi.cpp:701:11: warning: unused variable ‘c’ [-Wunused-variable]
       int c=0;
           ^
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<locus.size(); i++)
                 ~^~~~~~~~~~~~~
binput.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
binput.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
binput.cpp:186:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
binput.cpp:261:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    while (s<locus.size()) // for all SNPs
           ~^~~~~~~~~~~~~
binput.cpp:339:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        while (s<locus.size()) // for all SNPs
               ~^~~~~~~~~~~~~
binput.cpp:351:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     while (c<7 && s<locus.size())
                   ~^~~~~~~~~~~~~
binput.cpp:398:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(int l=0; l < locus.size(); l++)
                    ~~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<double>&, std::vector<double>&, std::vector<std::vector<double> >&)’:
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<std::vector<double> > msqrt(std::vector<std::vector<double> >&)’:
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<int>::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<int>::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<int>::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<int>::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<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i = 0; i < v.size(); i++)
                   ~~^~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<snpset.size(); l++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<include.size(); i++)
                 ~^~~~~~~~~~~~~~~
tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
tinput.cpp:246:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
tinput.cpp:256:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
tinput.cpp:261:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::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<Locus*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
tinput.cpp:591:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       if ( gn != 2 * sample.size() )
            ~~~^~~~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<sample.size(); i++)
                  ~^~~~~~~~~~~~~~
filters.cpp:123:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<sample.size();i++)
                 ~^~~~~~~~~~~~~~
filters.cpp:132:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0; l<locus.size();l++)
                      ~^~~~~~~~~~~~~
filters.cpp:155:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<sample.size();i++)
                 ~^~~~~~~~~~~~~~
filters.cpp:163:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0; l<locus.size();l++)
                      ~^~~~~~~~~~~~~
filters.cpp:198:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<sample.size();i++)
                 ~^~~~~~~~~~~~~~
filters.cpp:273:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<tokens.size(); i++)
                      ~^~~~~~~~~~~~~~
filters.cpp:249:14: warning: unused variable ‘freq’ [-Wunused-variable]
       double freq;
              ^~~~
filters.cpp:250:11: warning: unused variable ‘nm’ [-Wunused-variable]
       int nm;
           ^~
filters.cpp:591:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hetlist.size(); i++)
                     ~^~~~~~~~~~~~~~~
filters.cpp:611:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<no_founders_found_list.size(); i++)
                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filters.cpp:739:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::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<Individual*>::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<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0; l<locus.size();l++)
                      ~^~~~~~~~~~~~~
filters.cpp:1091:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0; l<locus.size();l++)
                      ~^~~~~~~~~~~~~
filters.cpp:1143:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<locus.size(); l++)
                     ~^~~~~~~~~~~~~
filters.cpp:1165:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int i=0; i<sample.size(); i++)
                       ~^~~~~~~~~~~~~~
filters.cpp:1257:7: warning: unused variable ‘tmp’ [-Wunused-variable]
   int tmp = deleteSNPs(del);
       ^~~
filters.cpp: In member function ‘void Plink::thinSNPs()’:
filters.cpp:1277:7: warning: unused variable ‘x’ [-Wunused-variable]
   int x = 0;
       ^
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::readTagFile()’:
prephap.cpp:226:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<char>::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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int s=0;s<S.size();s++)
                 ~^~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::makeSlidingWindow(std::__cxx11::string)’:
prephap.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tok.size(); i++)
                 ~^~~~~~~~~~~
prephap.cpp:560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<spec.size(); i++)
                 ~^~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<chrs.size();i++)
                ~^~~~~~~~~~~~
genome.cpp:1189:7: warning: unused variable ‘win_end’ [-Wunused-variable]
   int win_end = win_start + par::prune_ld_win;
       ^~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
assoc.cpp: In member function ‘void Plink::calcAssociationWithPermutation(Perm&)’:
assoc.cpp:395:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<pS->profileSNPs.size(); i++)
                  ~^~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:741:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int j=0; j<pS->selectedSNPs[l].size(); j++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:744:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pS->pv_set.size();i++)
                    ~^~~~~~~~~~~~~~~~~~
assoc.cpp:788:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0;j<pS->pv_set[i].size();j++)
                 ~^~~~~~~~~~~~~~~~~~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1536:11: warning: unused variable ‘best’ [-Wunused-variable]
       int best = 0 ;
           ^~~~
assoc.cpp: In member function ‘std::vector<double> Plink::testAssoc(int&, int&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, 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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from phase.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
phase.cpp: In member function ‘vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)’:
phase.cpp:373:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<t.size(); i++)
                      ~^~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::enumerateHaplotypes(std::vector<int>&)’:
phase.cpp:472:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   while (h<nh)
          ~^~~
phase.cpp: In member function ‘void HaploPhase::performAlternEM()’:
phase.cpp:678:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for (int z=0; z<currentStub.size(); z++)
                       ~^~~~~~~~~~~~~~~~~~~
phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::vector<int>, 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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
                  ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1280:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int z=0; z<hap1[i].size(); z++)
                      ~^~~~~~~~~~~~~~~
phase.cpp:1299:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
                  ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1575:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::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<int>::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<double>::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<int>&)’:
phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int z = 0; z < h1.size(); z++)
                       ~~^~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<original.size();i++)
                 ~^~~~~~~~~~~~~~~~
output.cpp:86:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<original[i].size(); j++)
                     ~^~~~~~~~~~~~~~~~~~~
output.cpp:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int k=0; k<maxr2.size(); k++)
                  ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_twolocus()’:
output.cpp:402:28: warning: variable ‘loc1’ set but not used [-Wunused-but-set-variable]
   vector<Locus*>::iterator loc1 = locus.begin()+m1;
                            ^~~~
output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable]
   vector<Locus*>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int s=0; s<setname.size(); s++)
                     ~^~~~~~~~~~~~~~~
output.cpp:526:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0; l<snpset[s].size(); l++)
                      ~^~~~~~~~~~~~~~~~~
output.cpp:553:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<lst.size(); l++)
                     ~^~~~~~~~~~~
output.cpp: In member function ‘void Plink::keep2SetsForGenome()’:
output.cpp:788:7: warning: unused variable ‘n_removed’ [-Wunused-variable]
   int n_removed = deleteIndividuals(del);
       ^~~~~~~~~
output.cpp: In member function ‘void Plink::outputSetFile()’:
output.cpp:2200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<snpset.size();i++)
                 ~^~~~~~~~~~~~~~
output.cpp:2322:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int j=0; j<inSet.size(); j++)
                 ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::setTable()’:
output.cpp:2367:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<setname.size();i++)
                    ~^~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::writeSetFile()’:
output.cpp:2409:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int j=0; j<snpset.size(); j++)
                 ~^~~~~~~~~~~~~~
output.cpp:2412:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<snpset[j].size(); l++)
                     ~^~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_pairList()’:
output.cpp:144:54: warning: ‘i1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
                                              ~~~~~~~~^~~~~~~~~~~~
output.cpp:145:54: warning: ‘i2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
                                              ~~~~~~~~^~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_indivReport()’:
output.cpp:69:25: warning: ‘i1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   << setw(6) << genotype(*this,i1,l) << "\n";
                 ~~~~~~~~^~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<klist[k]->person.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<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
tdt.cpp:144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<pS->profileSNPs.size(); i++)
                  ~^~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
tdt.cpp:327:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int j=0; j<pS->selectedSNPs[l].size(); j++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:330:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pS->pv_set.size();i++)
                    ~^~~~~~~~~~~~~~~~~~
tdt.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0;j<pS->pv_set[i].size();j++)
                 ~^~~~~~~~~~~~~~~~~~~~~
tdt.cpp: In member function ‘std::vector<double> Plink::testTDT(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
tdt.cpp:557:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<kid.size(); c++)
                  ~^~~~~~~~~~~
tdt.cpp:668:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int f=0; f<family.size(); f++)
                  ~^~~~~~~~~~~~~~
tdt.cpp:776:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int f=0; f<family.size(); f++)
                  ~^~~~~~~~~~~~~~
tdt.cpp:936:41: warning: ‘zt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ;
                                      ~~~^~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int j=0; j<s.size(); j++)
                 ~^~~~~~~~~
perm.cpp:145:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int k=0; k<s[j].size(); k++)
                   ~^~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::setOriginalRanking(vector_t&)’:
perm.cpp:187:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<original.size(); i++)
                 ~^~~~~~~~~~~~~~~~
perm.cpp:199:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int i=0; i<original.size(); i++)
                ~^~~~~~~~~~~~~~~~
perm.cpp: In member function ‘bool Perm::update(std::vector<double>&, std::vector<double>&)’:
perm.cpp:273:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
sets.cpp: In member function ‘void Set::sizeSets()’:
sets.cpp:37:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int s=0;s<snpset.size();s++)
               ~^~~~~~~~~~~~~~
sets.cpp:52:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(int i=0;i<snpset.size();i++)
                   ~^~~~~~~~~~~~~~
sets.cpp:59:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int i=0;i<snpset.size();i++)
               ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneMC(Plink&, bool, double)’:
sets.cpp:129:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<snpset.size(); s++)
                 ~^~~~~~~~~~~~~~
sets.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int s=0; s<snpset.size(); s++)
                     ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::dropNotSet(Plink&)’:
sets.cpp:216:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<snpset.size();i++)
                ~^~~~~~~~~~~~~~
sets.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<snpset.size();i++)
                ~^~~~~~~~~~~~~~
sets.cpp:237:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<snpset.size();i++)
                ~^~~~~~~~~~~~~~
sets.cpp:323:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::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<int>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<snpset.size();i++)
                    ~^~~~~~~~~~~~~~
sets.cpp:370:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<snpset.size();i++)
                ~^~~~~~~~~~~~~~
sets.cpp:413:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<stat_set.size();i++)
                    ~^~~~~~~~~~~~~~~~
sets.cpp:619:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int j=0;j<stat_set[i].size();j++)
               ~^~~~~~~~~~~~~~~~~~~
sets.cpp:631:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pv_set.size();i++)
                    ~^~~~~~~~~~~~~~
sets.cpp:632:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int j=0;j<pv_set[i].size();j++)
               ~^~~~~~~~~~~~~~~~~
sets.cpp:642:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pv_set.size();i++)
                    ~^~~~~~~~~~~~~~
sets.cpp:643:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int j=0;j<pv_set[i].size();j++)
               ~^~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::profileTestScore()’:
sets.cpp:703:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<snpset.size(); i++)
                 ~^~~~~~~~~~~~~~
sets.cpp:713:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<profileSNPs[i].size(); j++)
                     ~^~~~~~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitLDSetTest(vector_t&, bool)’:
sets.cpp:905:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<snpset.size(); i++)
                 ~^~~~~~~~~~~~~~
sets.cpp:975:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int k=0; k<selected.size(); k++)
                  ~^~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitStepwiseModel()’:
sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<snpset.size(); i++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<double>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0;i<ids.size();i++)
                  ~^~~~~~~~~~~
cluster.cpp:511:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0;i<val.size();i++)
                  ~^~~~~~~~~~~
cluster.cpp:492:8: warning: unused variable ‘size’ [-Wunused-variable]
    int size = peeps.size();
        ^~~~
cluster.cpp:626:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for ( int i = 4; i<tokens.size(); i++)
                     ~^~~~~~~~~~~~~~
cluster.cpp:648:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0;i<tokens.size();i++)
                  ~^~~~~~~~~~~~~~
cluster.cpp:784:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<mdist.size();i++)
                    ~^~~~~~~~~~~~~
cluster.cpp:786:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0;j<mdist.size();j++)
                 ~^~~~~~~~~~~~~
cluster.cpp:919:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int k=0;k<min_dst[0].size();k++)
               ~^~~~~~~~~~~~~~~~~~
cluster.cpp:954:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<cl.size(); i++)
                     ~^~~~~~~~~~
cluster.cpp:955:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int j=0; j<cl[i].size(); j++)
                ~^~~~~~~~~~~~~
cluster.cpp:975:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<cl.size()-1; i++)
                  ~^~~~~~~~~~~~
cluster.cpp:976:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int j=i+1; j<cl.size(); j++)
                      ~^~~~~~~~~~
cluster.cpp:990:34: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for(int j=0;j<cl[jmin].size();j++)
                ~^~~~~~~~~~~~~~~~
cluster.cpp:1041:33: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<int> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<cl.size(); i++)
                  ~^~~~~~~~~~
cluster.cpp:1050:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int j=0; j<cl[i].size(); j++)
                    ~^~~~~~~~~~~~~
cluster.cpp:1060:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j1=0; j1<sol.size(); j1++)
                   ~~^~~~~~~~~~~
cluster.cpp:1061:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int j2=0; j2<sol.size(); j2++)
                     ~~^~~~~~~~~~~
cluster.cpp:1107:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<cl.size(); i++)
                  ~^~~~~~~~~~
cluster.cpp:1110:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int j=0; j<cl[i].size(); j++)
                      ~^~~~~~~~~~~~~
cluster.cpp:1133:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0; j<sol.size(); j++)
                  ~^~~~~~~~~~~
cluster.cpp:1163:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<sol.size(); j++)
                     ~^~~~~~~~~~~
cluster.cpp:1169:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<sol[0].size(); i++)
                  ~^~~~~~~~~~~~~~
cluster.cpp: In function ‘double cldist(std::vector<std::vector<double> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<a.size(); i++)
                 ~^~~~~~~~~
cluster.cpp:1204:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int j=0; j<b.size(); j++)
                   ~^~~~~~~~~
cluster.cpp: In function ‘double groupAvgLink(std::vector<std::vector<double> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<a.size(); i++)
                 ~^~~~~~~~~
cluster.cpp:1229:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int j=0; j<b.size(); j++)
                   ~^~~~~~~~~
cluster.cpp: In function ‘bool homogeneous_clusters(Plink&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<a.size(); i++)
                 ~^~~~~~~~~
cluster.cpp:1255:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int j=0; j<b.size(); j++)
                   ~^~~~~~~~~
cluster.cpp: In function ‘bool spec_clusters(Plink&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<a.size(); i++)
                 ~^~~~~~~~~
cluster.cpp:1276:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int j=0; j<b.size(); j++)
                 ~^~~~~~~~~
cluster.cpp: In function ‘bool pairable_cluster(std::vector<std::vector<bool> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<a.size(); i++)
                 ~^~~~~~~~~
cluster.cpp:1291:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int j=0; j<b.size(); j++)
                   ~^~~~~~~~~
cluster.cpp: In member function ‘void Plink::groupGenome()’:
cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for ( int i = 4; i<tokens.size(); i++)
                    ~^~~~~~~~~~~~~~
cluster.cpp:1661:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<tokens.size();i++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
In file included from plink.cpp:40:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int k=0; k<values.size(); k++)
                   ~^~~~~~~~~~~~~~
plink.cpp: In function ‘int main(int, char**)’:
plink.cpp:763:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
       par::make_founders &&
       ~~~~~~~~~~~~~~~~~~~^~
       !par::built_families)
       ~~~~                
plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<chrs.size();i++)
                ~^~~~~~~~~~~~
plink.cpp: In member function ‘void Plink::cleanUp()’:
plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
plink.cpp:2362:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<locus.size(); l++)
                 ~^~~~~~~~~~~~~
plink.cpp:2366:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int l=0; l<SNP.size(); l++)
                   ~^~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<P.sample.size(); i++)
                 ~^~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector<bool>&, std::vector<bool>&, std::vector<bool>&, std::map<Individual*, int>&)’:
genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int k=0; k<person->kids.size(); k++)
                 ~^~~~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
haploCC.cpp: In member function ‘void HaploPhase::haplotypicCC(std::map<int, int>&, int, bool)’:
haploCC.cpp:48:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::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<int>::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<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<double>&, std::__cxx11::string)’:
multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<chi.size(); l++)
                 ~^~~~~~~~~~~
multiple.cpp:131:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Pair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<schi.size(); i++)
                 ~^~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<snpset.size(); s++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int c=0; c<f->kid.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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int k=0; k<mf->kid.size(); k++)
                      ~^~~~~~~~~~~~~~~
trio.cpp:272:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int k=0; k<mf->kid.size(); k++)
                      ~^~~~~~~~~~~~~~~
trio.cpp:335:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::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<Individual*>::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<Individual*>::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<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int f=0; f<family.size(); f++)
                 ~^~~~~~~~~~~~~~
trio.cpp:474:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int f=0; f<family.size(); f++)
                 ~^~~~~~~~~~~~~~
trio.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
trio.cpp:504:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<kid.size(); c++)
                  ~^~~~~~~~~~~
trio.cpp:871:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
trio.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
trio.cpp:895:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<kid.size(); c++)
                      ~^~~~~~~~~~~
trio.cpp:931:6: warning: unused variable ‘tmp’ [-Wunused-variable]
  int tmp = deleteSNPs(mendel_locus);
      ^~~
trio.cpp:936:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0;f<family.size();f++)
                    ~^~~~~~~~~~~~~~
trio.cpp:943:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<family[f]->kid.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<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int f=0; f<family.size(); f++)
                 ~^~~~~~~~~~~~~~
trio.cpp:1048:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int c=0; c<kid.size(); c++)
                     ~^~~~~~~~~~~
trio.cpp: In member function ‘void Plink::makeMissingParents()’:
trio.cpp:1236:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for ( int k=0; k<person->pm->kids.size(); k++)
                   ~^~~~~~~~~~~~~~~~~~~~~~~~
trio.cpp:1245:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for ( int k=0; k<person->pp->kids.size(); k++)
                   ~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
poo.cpp:195:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pS->pv_set.size();i++)
                    ~^~~~~~~~~~~~~~~~~~
poo.cpp:198:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0;j<pS->pv_set[i].size();j++)
                 ~^~~~~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘std::vector<double> Plink::testTDT_POO(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
poo.cpp:293:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
poo.cpp:328:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<kid.size(); c++)
                  ~^~~~~~~~~~~
poo.cpp:239:10: warning: unused variable ‘zt’ [-Wunused-variable]
   double zt;
          ^~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_IxJxK(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:747:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<X.size(); i++)
                 ~^~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_ORD(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<X.size(); i++)
                 ~^~~~~~~~~
mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<snpset.size(); s++)
                 ~^~~~~~~~~~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:489:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int l=0; l<P.snpset[s1].size(); l++)
                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:497:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int l=0; l<P.snpset[s2].size(); l++)
                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:506:10: warning: unused variable ‘n12’ [-Wunused-variable]
      int n12 = n1 + n2;
          ^~~
genepi.cpp:507:10: warning: unused variable ‘ne’ [-Wunused-variable]
      int ne = n1 < n2 ? n1 : n2;
          ^~
genepi.cpp: In function ‘void CCA_caseonly(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:1025:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int l=0; l<P.snpset[s1].size(); l++)
                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:1033:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int l=0; l<P.snpset[s2].size(); l++)
                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:1043:10: warning: unused variable ‘n12’ [-Wunused-variable]
      int n12 = n1 + n2;
          ^~~
genepi.cpp:1044:10: warning: unused variable ‘ne’ [-Wunused-variable]
      int ne = n1 < n2 ? n1 : n2;// ne = min(p,q)
          ^~
genepi.cpp:1064:10: warning: unused variable ‘nind’ [-Wunused-variable]
      int nind = calcGENEPIMeanVariance(pSNP,
          ^~~~
genepi.cpp: In function ‘int calcGENEPIMeanVariance(std::vector<CSNP*>&, int, int, bool, Plink*, std::vector<double>&, std::vector<std::vector<double> >&, std::vector<Individual*>&, std::vector<int>&, std::vector<int>&)’:
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<std::vector<int> >&, 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=/<<PKGBUILDDIR>>=. -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
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
webcheck.cpp:130:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<Y.size(); i++)
                 ~^~~~~~~~~
linear.cpp: In member function ‘double LinearModel::getPValue()’:
linear.cpp:734:8: warning: unused variable ‘okay’ [-Wunused-variable]
   bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid;
        ^~~~
linear.cpp: In function ‘void gaussj(matrix_t&, matrix_t&)’:
linear.cpp:100:13: warning: ‘irow’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     indxr[i]=irow;
linear.cpp:96:5: warning: ‘icol’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (irow != icol) {
     ^~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >&)’:
helper.cpp:58:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<s.size(); i++)
                 ~^~~~~~~~~
helper.cpp: In function ‘std::__cxx11::string displayLine(std::vector<std::__cxx11::basic_string<char> >&)’:
helper.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<s.size(); i++)
                 ~^~~~~~~~~
helper.cpp: In function ‘void display(matrix_t&)’:
helper.cpp:76:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::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<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<m[i].size(); j++)
                     ~^~~~~~~~~~~~
helper.cpp: In function ‘void display(vector_t&)’:
helper.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i< m.size(); i++)
                 ~^~~~~~~~~~
helper.cpp: In function ‘void display(std::vector<int>&)’:
helper.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int t=0; t<tokens.size(); t++)
                     ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > CArgs::value(std::__cxx11::string, int)’:
helper.cpp:267:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> > parse2str(std::__cxx11::string)’:
helper.cpp:306:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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<char>::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<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  if (i == s.length()-1) t += s[i];
      ~~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> parse2int(std::__cxx11::string)’:
helper.cpp:323:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<v.size(); i++)
                 ~^~~~~~~~~
helper.cpp: In member function ‘void CArgs::check_unused_options(Plink&)’:
helper.cpp:461:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=1; i<original.size(); i++)
                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void summaryBasics(Plink&)’:
helper.cpp:595:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<P.sample.size(); i++)
                     ~^~~~~~~~~~~~~~~~
helper.cpp:611:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<P.sample.size(); i++)
                     ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘double genotypingRate(Plink&, int)’:
helper.cpp:659:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<P.sample.size();i++)
                    ~^~~~~~~~~~~~~~~~
helper.cpp:664:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<P.sample.size();i++)
                    ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > listPossibleHaplotypes(Plink&, std::vector<int>)’:
helper.cpp:709:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   while(h<nh)
         ~^~~
helper.cpp:729:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int h=0; h<hap.size(); h++)
                 ~^~~~~~~~~~~
helper.cpp: In function ‘void removeMissingPhenotypes(Plink&)’:
helper.cpp:775:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<P.sample.size(); i++)
                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void geno2matrix(std::vector<int>&, matrix_t&, boolmatrix_t&, bool)’:
helper.cpp:795:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<std::__cxx11::basic_string<char> >::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<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<P.locus.size();i++)
                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘int getMarkerNumber(Plink&, std::__cxx11::string)’:
helper.cpp:966:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<P.locus.size();i++)
                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘bool seeChromosome(Plink&, int)’:
helper.cpp:973:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0;l<P.locus.size();l++)
                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> getChromosomeMarkerRange(Plink&, int)’:
helper.cpp:989:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<P.locus.size();i++)
                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> getChromosomeRange(Plink&)’:
helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<P.locus.size();i++)
                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘void checkFileExists(std::vector<std::__cxx11::basic_string<char> >)’:
helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int k=0; k<f.size(); k++)
                 ~^~~~~~~~~
helper.cpp: In member function ‘void Plink::prettyPrintLengths()’:
helper.cpp:1264:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::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<char>::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<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
     if (locus[l]->name.length() > par::pp_maxsnp)
         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
helper.cpp: In function ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1389:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<u.size(); i++)
                  ~^~~~~~~~~
helper.cpp:1391:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int j=0; j<u[i].size(); j++)
                      ~^~~~~~~~~~~~
helper.cpp: In member function ‘int Plink::deleteSNPs(std::vector<bool>&)’:
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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp:2462:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<filters.size(); j++)
                     ~^~~~~~~~~~~~~~~
helper.cpp:2491:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnCase()’:
helper.cpp:2510:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnControl()’:
helper.cpp:2530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnMale()’:
helper.cpp:2549:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnFemale()’:
helper.cpp:2568:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnFounder()’:
helper.cpp:2587:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnNonFounder()’:
helper.cpp:2606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::attribFilterSNP()’:
helper.cpp:2638:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<vlist.size(); i++)
                 ~^~~~~~~~~~~~~
helper.cpp:2671:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=1; j<tok.size(); j++)
                     ~^~~~~~~~~~~
helper.cpp: In member function ‘void Plink::attribFilterInd()’:
helper.cpp:2722:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<vlist.size(); i++)
                 ~^~~~~~~~~~~~~
helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=1; j<tok.size(); j++)
                     ~^~~~~~~~~~~
helper.cpp: In function ‘void makePersonMap(Plink&, std::map<std::__cxx11::basic_string<char>, Individual*>&)’:
helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<P.sample.size(); i++)
                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void smoother(Plink&, vector_t&, int, vector_t&, vector_t&, std::vector<int>&)’:
helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if ( input.size() != P.nl_all )
        ~~~~~~~~~~~~~^~~~~~~~~~~
helper.cpp: In function ‘std::map<std::__cxx11::basic_string<char>, std::set<Range> > readRange(std::__cxx11::string)’:
helper.cpp:3097:20: warning: unused variable ‘s’ [-Wunused-variable]
       set<Range> * 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<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
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;
            ^~
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<std::__cxx11::basic_string<char> >::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<Individual*>::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<Individual*>::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<Individual*>::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<Family*>::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<Family*>::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<int>&, std::ofstream&, bool, Perm&, std::vector<int>&, std::vector<bool>&)’:
qfam.cpp:505:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::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<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<family.size(); i++)
                 ~^~~~~~~~~~~~~~
qfam.cpp:657:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int f=0; f<pbetween.size(); f++)
                 ~^~~~~~~~~~~~~~~~
qfam.cpp:639:10: warning: unused variable ‘tc’ [-Wunused-variable]
      int tc = 0;
          ^~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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;
              ~~~~~~~~~~~~^~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<Y.size(); i++)
                 ~^~~~~~~~~
logistic.cpp: In member function ‘double LogisticModel::getPValue()’:
logistic.cpp:327:8: warning: unused variable ‘okay’ [-Wunused-variable]
   bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid;
        ^~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<include.size(); i++)
                 ~^~~~~~~~~~~~~~~
merge.cpp:377:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<locus2.size(); l++)
                 ~^~~~~~~~~~~~~~
merge.cpp:395:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0;l<locus.size();l++)
                ~^~~~~~~~~~~~~
merge.cpp:403:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0;l<locus.size();l++)
                     ~^~~~~~~~~~~~~
merge.cpp:426:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<locus2.size()-exist_cnt; i++)
                     ~^~~~~~~~~~~~~~~~~~~~~~~~
merge.cpp:722:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::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<bool>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<sample.size(); i++)
                   ~^~~~~~~~~~~~~~
merge.cpp:830:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<sample.size();i++)
                    ~^~~~~~~~~~~~~~
merge.cpp:842:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<sample.size(); i++)
                  ~^~~~~~~~~~~~~~
merge.cpp: In member function ‘bool Plink::reconcileMerge(int, int, std::__cxx11::string, std::__cxx11::string, bool, bool, std::ofstream&, std::map<std::__cxx11::basic_string<char>, int>&)’:
merge.cpp:1103:3: warning: ‘write’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (write)
   ^~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
mishap.cpp: In member function ‘void Plink::performMisHapTests()’:
mishap.cpp:209:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::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<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int z = 0 ; z < haplo->hap1[i].size(); z++)
                         ~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<pair1.size(); i++)
                 ~^~~~~~~~~~~~~
legacy.cpp:377:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<v_pihat.size();i++)
                    ~^~~~~~~~~~~~~~~
legacy.cpp:381:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pihat.size();i++)
                    ~^~~~~~~~~~~~~
legacy.cpp:384:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0;j<pihat[i].size();j++)
                 ~^~~~~~~~~~~~~~~~
legacy.cpp:390:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<phenotype.size();i++)
                    ~^~~~~~~~~~~~~~~~~
legacy.cpp:395:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<pihat_G.size();i++)
                    ~^~~~~~~~~~~~~~~
legacy.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<in_anal.size(); i++)
                 ~^~~~~~~~~~~~~~~
legacy.cpp:424:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<in_anal.size(); i++)
                 ~^~~~~~~~~~~~~~~
legacy.cpp:460:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<s.size(); j++)
                     ~^~~~~~~~~
legacy.cpp:461:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int k=0; k<s[j].size(); k++)
                ~^~~~~~~~~~~~
legacy.cpp:462:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<pin_anal.size(); i++)
                  ~^~~~~~~~~~~~~~~~
legacy.cpp:467:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<in_anal.size(); i++)
                     ~^~~~~~~~~~~~~~~
legacy.cpp:480:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<pair1.size(); i++)
                     ~^~~~~~~~~~~~~
legacy.cpp: In member function ‘void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)’:
legacy.cpp:203:18: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         << start - last - 1 << " ";
            ~~~~~~^~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
model.cpp: In member function ‘void Model::setMissing(std::vector<bool>&)’:
model.cpp:132:23: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::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<int>::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<std::vector<double> >::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<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::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<bool>::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<bool>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<sample.size(); i++)
                   ~^~~~~~~~~~~~~~
input.cpp:595:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<ambiguous.size(); i++)
                     ~^~~~~~~~~~~~~~~~~
input.cpp:611:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<sample.size();i++)
                ~^~~~~~~~~~~~~~
input.cpp:631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readSet()’:
input.cpp:695:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<snpset.size();i++)
                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readClusterFile(bool)’:
input.cpp:787:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:817:25: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i0=0; i0<tokens.size(); i0++)
                       ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readPhenoFile()’:
input.cpp:897:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:927:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for ( int i=2; i<tokens.size(); i++)
                   ~^~~~~~~~~~~~~~
input.cpp:961:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<sample.size(); i++)
                   ~^~~~~~~~~~~~~~
input.cpp:1043:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:1064:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::makePhenotype()’:
input.cpp:1208:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readCovariateFile()’:
input.cpp:1232:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:1256:25: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int i0=0; i0<tokens.size(); i0++)
                     ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readCovListFile()’:
input.cpp:1335:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:1374:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<covlist.size(); c++)
                  ~^~~~~~~~~~~~~~~
input.cpp:1538:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int c=0; c<covlist.size(); c++)
                     ~^~~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readMultiplePhenoFile()’:
input.cpp:1572:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:1599:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0;i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp:1745:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<phelist.size(); c++)
                  ~^~~~~~~~~~~~~~~
input.cpp:1764:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int c=0; c<phelist.size(); c++)
                     ~^~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readSegmentFile(std::ifstream&)’:
input.cpp:1792:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readMapFile(std::__cxx11::string, std::vector<bool>&, std::vector<int>&, int&)’:
input.cpp:2116:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<include.size(); i++)
                 ~^~~~~~~~~~~~~~~
input.cpp:2172:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
input.cpp:2200:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
input.cpp:2210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int j=0; j<ordered.size(); j++)
                     ~^~~~~~~~~~~~~~~
input.cpp:2215:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::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<Locus*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<sample.size(); i++)
                   ~^~~~~~~~~~~~~~
input.cpp:2397:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<sample.size();i++)
                ~^~~~~~~~~~~~~~
input.cpp:2419:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
input.cpp:2453:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<ambiguous.size(); i++)
                     ~^~~~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readHomozygSegmentFile(std::ifstream&)’:
input.cpp:2471:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::updateAlleles()’:
input.cpp:2732:12: warning: unused variable ‘success’ [-Wunused-variable]
       bool success = false;
            ^~~~~~~
input.cpp: In member function ‘void Plink::readData()’:
input.cpp:91:13: warning: ‘PED’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ( feof(PED) )
         ~~~~^~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
glm.cpp: In member function ‘vector_t Plink::glmAssoc(bool, Perm&)’:
glm.cpp:294:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<conditioner.size(); c++)
                      ~^~~~~~~~~~~~~~~~~~~
glm.cpp:355:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<conditioner.size(); c++)
                      ~^~~~~~~~~~~~~~~~~~~
glm.cpp:423:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int c=0; c<conditioner.size(); c++)
                  ~^~~~~~~~~~~~~~~~~~~
glm.cpp:610:28: warning: ‘df’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    double pvalue = chiprobP(chisq,df);
                    ~~~~~~~~^~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
dfam.cpp: In member function ‘std::vector<double> Plink::testSibTDT(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
dfam.cpp:86:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
               for ( int k=0; k<fam->kid.size(); k++)
                              ~^~~~~~~~~~~~~~~~
dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
               for ( int k=0; k<fam->kid.size(); k++)
                              ~^~~~~~~~~~~~~~~~
dfam.cpp:106:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int c=0; c<klist[k]->person.size(); c++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<family.size(); f++)
                     ~^~~~~~~~~~~~~~
dfam.cpp:239:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
        if ( pat1 && (!pat2) ||
             ~~~~~^~~~~~~~~~
dfam.cpp:271:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<family[f]->kid.size(); c++)
                      ~^~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:378:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int c=0; c<family[f]->kid.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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int c=0; c<klist[k]->person.size(); c++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:151:11: warning: unused variable ‘totalInformative’ [-Wunused-variable]
       int totalInformative = 0;
           ^~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
sockets.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > 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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
haploQTL.cpp: In member function ‘void HaploPhase::haplotypicQTL(std::map<int, int>&, int, bool)’:
haploQTL.cpp:83:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z = 0 ; z < hap1[i].size(); z++)
                     ~~^~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int i=25; i<tokens.size()-1; i++)
                     ~^~~~~~~~~~~~~~~~
lookup.cpp:203:8: warning: unused variable ‘totalSNPs’ [-Wunused-variable]
    int totalSNPs = 0;
        ^~~~~~~~~
lookup.cpp:204:8: warning: unused variable ‘gcount’ [-Wunused-variable]
    int gcount = 0;
        ^~~~~~
lookup.cpp:272:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=25; i<tokens.size()-1; i++)
                       ~^~~~~~~~~~~~~~~~
lookup.cpp:289:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=25; i<tokens.size()-1; i++)
                   ~^~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>&, std::vector<int>&, std::vector<int>&)’:
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<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0;i<pihat.size();i++)
                ~^~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::indivSegmentSummary()’:
segment.cpp:1855:14: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
    indivPair p = ic->first;
              ^
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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<ordered.size(); i++)
                 ~^~~~~~~~~~~~~~~
bmerge.cpp:390:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<locus2.size(); l++)
                 ~^~~~~~~~~~~~~~
bmerge.cpp:409:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0;l<locus.size();l++)
                ~^~~~~~~~~~~~~
bmerge.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int l=0;l<locus.size();l++)
                     ~^~~~~~~~~~~~~
bmerge.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<locus2.size()-exist_cnt; i++)
                     ~^~~~~~~~~~~~~~~~~~~~~~~~
bmerge.cpp:549:11: warning: variable ‘indn’ set but not used [-Wunused-but-set-variable]
       int indn = isample->second;
           ^~~~
bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       while (s<locus2.size()) // for all SNPs in second file
              ~^~~~~~~~~~~~~~
bmerge.cpp:692:14: warning: unused variable ‘snp’ [-Wunused-variable]
       CSNP * snp;
              ^~~
bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<sample.size(); i++)
                   ~^~~~~~~~~~~~~~
bmerge.cpp:871:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0;i<sample.size();i++)
                    ~^~~~~~~~~~~~~~
bmerge.cpp:883:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<sample.size(); i++)
                  ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<int>::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<double>::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<Range, int2>&)’:
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Locus*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<sample.size(); i++)
                     ~^~~~~~~~~~~~~~
linput.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<SNP.size(); l++)
                     ~^~~~~~~~~~~
linput.cpp:146:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<sample.size(); i++)
                      ~^~~~~~~~~~~~~~
linput.cpp:200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<include.size(); i++)
                 ~^~~~~~~~~~~~~~~
linput.cpp:209:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
In file included from genogroup.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::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<Segment*, std::less<Segment*> >::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<Segment*, std::less<Segment*> >::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<Segment*, std::less<Segment*> >::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<int>::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<int>::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<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from em.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
em.cpp: In member function ‘void HaploPhase::performEM_original()’:
em.cpp:89:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for (int z=0; z<hap1[i].size(); z++)
                       ~^~~~~~~~~~~~~~~
em.cpp:97:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for (int z=0; z<hap1[i].size(); z++)
                       ~^~~~~~~~~~~~~~~
em.cpp:106:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
em.cpp:128:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
em.cpp:132:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int z=0; z<hap1[i].size(); z++)
                 ~^~~~~~~~~~~~~~~
em.cpp:162:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for (int z=0; z<hap1[i].size(); z++)
                       ~^~~~~~~~~~~~~~~
em.cpp:166:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int z=0; z<hap1[i].size(); z++)
                     ~^~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from nonfounderphasing.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::phaseAndScoreNonfounder(int)’:
nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::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<FamilyTransmissions, double>&)’:
nonfounderphasing.cpp:715:14: warning: unused variable ‘posterior’ [-Wunused-variable]
       double posterior = ip->second;
              ^~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
pdriver.cpp: In member function ‘void Plink::proxyWrapper()’:
pdriver.cpp:266:11: warning: unused variable ‘similar’ [-Wunused-variable]
       int similar = 0;
           ^~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
In file included from haplowindow.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
haplowindow.cpp: In function ‘void verboseDisplayWindows2(HaploPhase*, int, bool)’:
haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<nh)
          ~^~~
haplowindow.cpp: In member function ‘void HaploWindow::prunePhase(int, double)’:
haplowindow.cpp:558:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<double>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
haplowindow.cpp:691:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
haplowindow.cpp:751:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int z=0; z<hap1[i].size(); z++)
                      ~^~~~~~~~~~~~~~~
haplowindow.cpp:791:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
haplowindow.cpp:798:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
haplowindow.cpp:868:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z=0; z<hap1[i].size(); z++)
                   ~^~~~~~~~~~~~~~~
haplowindow.cpp:872:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int z=0; z<hap1[i].size(); z++)
                 ~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::reportPhase()’:
haplowindow.cpp:949:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z2=0; z2<hap1[i].size(); z2++)
                    ~~^~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from impute.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
impute.cpp: In constructor ‘probabilisticGenotype::probabilisticGenotype()’:
impute.cpp:40:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     phased = genotype = false;
              ~~~~~~~~~^~~~~~~
impute.cpp: In member function ‘void HaploPhase::updateForImputation()’:
impute.cpp:105:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z=0; z<hap1[i].size(); z++)
                  ~^~~~~~~~~~~~~~~
impute.cpp:144:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<double>::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<int>::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<probabilisticGenotype>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int s=0; s < g.size(); s++)
                     ~~^~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from genoerr.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
genoerr.cpp: In member function ‘void HaploPhase::queryThisGenotype(int, int, int, vector_t&)’:
genoerr.cpp:157:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int z=0; z<hap1[i].size(); z++)
                 ~^~~~~~~~~~~~~~~
genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::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<int>::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<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int z2=0; z2<hap1[i].size(); z2++)
                       ~~^~~~~~~~~~~~~~~
genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z2=0; z2<new_hap1.size(); z2++)
                   ~~^~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseNumberList(std::__cxx11::string)’:
nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tok.size(); i++)
                 ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseStringList(std::__cxx11::string, std::map<std::__cxx11::basic_string<char>, int>*)’:
nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tok.size(); i++)
                 ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::expandNumberList(std::vector<int>&)’:
nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<nlist.size(); i++)
                 ~^~~~~~~~~~~~~
nlist.cpp:124:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<nlist.size(); i++)
                 ~^~~~~~~~~~~~~
nlist.cpp:151:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<n.size(); i++)
                 ~^~~~~~~~~
nlist.cpp:160:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<n.size(); i++)
                     ~^~~~~~~~~
nlist.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > NList::tokenize(std::__cxx11::string)’:
nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<s.length(); i++)
                 ~^~~~~~~~~~~
nlist.cpp:239:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       else if ( i == s.length()-1 )
                 ~~^~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
In file included from metaem.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
metaem.cpp: In member function ‘void HaploPhase::enumeratePhasedWindows(int)’:
metaem.cpp:239:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
    while (h<nperm)
           ~^~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
In file included from haplohelper.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<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int i=0; i<g.size(); i++)
                   ~^~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::imputeAllHaplotypes()’:
haplohelper.cpp:104:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<new_one[i].size(); l++)
                     ~^~~~~~~~~~~~~~~~~~
haplohelper.cpp:134:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l < actual_map.size(); l++)
                 ~~^~~~~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > HaploPhase::returnHaplotypes(std::vector<int>&)’:
haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int h=0; h<hap.size(); h++)
                 ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::setTestHaplotype(std::__cxx11::string)’:
haplohelper.cpp:337:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int h=0; h<hap.size(); h++)
                 ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhase()’:
haplohelper.cpp:396:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int z2=0; z2<hap1[i].size(); z2++)
                    ~~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhaseWideFormat()’:
haplohelper.cpp:487:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int z=0; z<hap1[i].size(); z++)
                 ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::imputeHaplotypes(int, bool&, bool&)’:
haplohelper.cpp:754:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int z=0; z<hap1[i].size(); z++)
                     ~^~~~~~~~~~~~~~~
haplohelper.cpp:802:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int z=0; z<hap1[i].size(); z++)
                  ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::rsq_internal(boolvec_t&, boolvec_t&, boolvec_t&, boolvec_t&)’:
haplohelper.cpp:850:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::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<bool>::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<bool>::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<bool>::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<bool>::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<bool>::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<int>::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<int>::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<int>::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<int>&)’:
haplohelper.cpp:1419:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::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<double>::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<int>::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
greport.cpp:147:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
proxy.cpp: In member function ‘void Plink::performProxyTests(int)’:
proxy.cpp:314:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=1; i<proxyHaplotypePlusSNP.size(); i++)
                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:332:22: warning: comparison of integer expressions of different signedness: ‘std::set<int>::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<int>::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<int>::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<std::vector<int> >::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=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int s=0; s<snpset.size(); s++)
                     ~^~~~~~~~~~~~~~
profile.cpp:402:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int s=0; s<snpset.size(); s++)
                  ~^~~~~~~~~~~~~~
profile.cpp:421:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if ( qcnt == qlabel.size() )
        ~~~~~^~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::calculateProfile(std::map<int, double>&, std::map<int, bool>&, vector_t&, matrix_t&, std::vector<int>&, std::vector<int>&)’:
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<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=0; j<snpset.size(); j++)
                  ~^~~~~~~~~~~~~~
profile.cpp: In function ‘void scoreRanges(int, std::vector<int>&, std::map<int, std::set<Range*> >&, std::map<Range*, int>&, std::ofstream&)’:
profile.cpp:667:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0; l<f.size(); l++)
                 ~^~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::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<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i = 0 ; i < inds.size() ; i++)
                        ~~^~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
clumpld.cpp: In member function ‘std::vector<ResultTrio> clump_LD::read_assoc_file(std::__cxx11::string)’:
clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int f=0; f<filename.size(); f++)
                 ~^~~~~~~~~~~~~~~~
clumpld.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<tokens.size(); i++)
                     ~^~~~~~~~~~~~~~
clumpld.cpp:137:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for ( int f=0; f<tok_annot.size(); f++)
                     ~^~~~~~~~~~~~~~~~~
clumpld.cpp:173:23: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int f=0; f<annot_field.size(); f++)
                      ~^~~~~~~~~~~~~~~~~~~
clumpld.cpp:204:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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<ResultTrio>::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<Locus*>::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<int2, double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
               if( j < grouped_snps.size()-1)
                   ~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -g  -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp
In file included from 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<std::__cxx11::basic_string<char> >::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<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<sp.size(); s++)
                 ~^~~~~~~~~~
simul.cpp:679:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<sp.size(); s++)
                 ~^~~~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs_QT()’:
simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<sp.size(); s++)
                 ~^~~~~~~~~~
simul.cpp:1211:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int s=0; s<sp.size(); s++)
                 ~^~~~~~~~~~
simul.cpp:1358:23: warning: unused variable ‘cumU’ [-Wunused-variable]
      double cumA = 0, cumU = 0;
                       ^~~~
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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
setscreen.cpp:110:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::vector<int> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i < snpset[j].size(); i++)
                     ~~^~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
blox.cpp: In member function ‘std::map<Range, std::vector<int> > 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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int k=0; k<b.size(); k++)
                     ~^~~~~~~~~
blox.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int k=0; k<b.size(); k++)
                     ~^~~~~~~~~
blox.cpp:123:16: warning: unused variable ‘fourGameteCutoff’ [-Wunused-variable]
   const double fourGameteCutoff = 0.01;
                ^~~~~~~~~~~~~~~~
blox.cpp: In member function ‘void PairwiseLinkage::calculateCI()’:
blox.cpp:469:7: warning: unused variable ‘total_chroms’ [-Wunused-variable]
   int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH;
       ^~~~~~~~~~~~
blox.cpp:569:41: warning: ‘pB2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if ( pB1>0 ) 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;
          ^~
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int t = 0 ; t < tokens.size() ; t++)
                     ~~^~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<locus.size(); l++)
                     ~^~~~~~~~~~~~~
gvar.cpp:192:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<locus.size(); l++)
                     ~^~~~~~~~~~~~~
gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
gvar.cpp:298:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<sample.size(); i++)
                  ~^~~~~~~~~~~~~~
gvar.cpp:381:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<include.size(); i++)
                     ~^~~~~~~~~~~~~~~
gvar.cpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<include.size(); i++)
                     ~^~~~~~~~~~~~~~~
gvar.cpp:403:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<sample.size(); i++)
                 ~^~~~~~~~~~~~~~
gvar.cpp:471:11: warning: unused variable ‘ip’ [-Wunused-variable]
       int ip = peri->second;
           ^~
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<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<locus.size(); l++)
                     ~^~~~~~~~~~~~~
gvar.cpp:553:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int l=0; l<SNP.size(); l++)
                ~^~~~~~~~~~~
gvar.cpp:556:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int i=0; i<sample.size(); i++)
                ~^~~~~~~~~~~~~~
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;
                           ^~~~
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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
whap.cpp: In member function ‘vector_t Plink::conditionalHaplotypeTest(bool, Perm&)’:
whap.cpp:334:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::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<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int g=0; g<subnullModel.group.size(); g++)
                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:454:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int h=0; h<coeff1.size(); h++)
                     ~^~~~~~~~~~~~~~
whap.cpp:456:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int h=0; h<coeff0.size(); h++)
                     ~^~~~~~~~~~~~~~
whap.cpp:508:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for ( int g=0; g<nullModel.group.size(); g++ )
                  ~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:511:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for ( int g2=0; g2<alternateModel.group.size(); g2++ )
                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:619:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::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<int>::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<double>::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<double>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int h=0; h<tok.size(); h++)
                     ~^~~~~~~~~~~
whap.cpp:986:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<tok.size(); i++)
                     ~^~~~~~~~~~~
whap.cpp:1015:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char>, 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<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<lst.size(); i++)
                  ~^~~~~~~~~~~
whap.cpp:1162:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<lst.size(); i++)
                      ~^~~~~~~~~~~
whap.cpp:1197:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<snplist.size(); i++)
                     ~^~~~~~~~~~~~~~~
whap.cpp:1231:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<lst.size(); i++)
                  ~^~~~~~~~~~~
whap.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::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<int>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int l=0; l<lst.size(); l++)
                     ~^~~~~~~~~~~
whap.cpp: In member function ‘void Chap::setSNPList(std::vector<int>&, ChapModel&)’:
whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int l=0;l<snplist.size(); l++)
                ~^~~~~~~~~~~~~~~
whap.cpp: In function ‘void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)’:
whap.cpp:1425:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    if ( cnt>0 && cnt2 < m.group[h].size() )
                  ~~~~~^~~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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;
          ^~
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<std::__cxx11::basic_string<char> >::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<Range,string>::iterator is = idescription.find(*ir);
                                    ^~
cnv.cpp:815:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Segment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int s1=0; s1<segment.size(); s1++)
                      ~~^~~~~~~~~~~~~~~
cnv.cpp:825:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Segment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int s2=s1+1; s2<segment.size(); s2++)
                      ~~^~~~~~~~~~~~~~~
cnv.cpp:916:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  if ( par::cnv_freq_include )
  ^~
cnv.cpp:922:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
    isection.clear();
    ^~~~~~~~
cnv.cpp:1031:25: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable]
    set<Range>::iterator i2 = isection.begin();
                         ^~
cnv.cpp:1103:36: warning: variable ‘il’ set but not used [-Wunused-but-set-variable]
    map<indivPair,double>::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<Range>&, 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<int, CInfo>::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]
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j=1; j<tok.size(); j++)
                  ~^~~~~~~~~~~
annot.cpp:149:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<tokens.size(); i++)
                 ~^~~~~~~~~~~~~~
annot.cpp:250:23: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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;
         ^~~~~~~
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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<ns.size(); f++)
                     ~^~~~~~~~~~
metaanal.cpp:182:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int f=0; f<ns.size(); f++)
                     ~^~~~~~~~~~
metaanal.cpp:203:18: warning: statement has no effect [-Wunused-value]
     par::run_chr == -1;
     ~~~~~~~~~~~~~^~~~~
metaanal.cpp:213:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<tok.size(); i++)
                  ~^~~~~~~~~~~
metaanal.cpp:235:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<tokens.size(); i++)
                     ~^~~~~~~~~~~~~~
metaanal.cpp:300:23: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int f=0; f<par::meta_files.size(); f++)
                   ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:637:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int f=0; f<par::meta_files.size(); f++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:680:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
      for (int f=0; f<par::meta_files.size(); f++)
                    ~^~~~~~~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<hap.size(); i++)
                     ~^~~~~~~~~~~
dosage.cpp: In member function ‘void Plink::processDosageFile()’:
dosage.cpp:110:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double2>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<dosageFilename_all.size(); i++)
                  ~^~~~~~~~~~~~~~~~~~~~~~~~~~
dosage.cpp:548:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ZInput*>::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=firstCol; i<tok.size(); i+= 2 )
                         ~^~~~~~~~~~~
dosage.cpp:695:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, 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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int q=0; q<inQ.size(); q++)
                   ~^~~~~~~~~~~
dosage.cpp:1170:11: warning: unused variable ‘statistic’ [-Wunused-variable]
    double statistic = valid ? model->getStatistic() : 0;
           ^~~~~~~~~
dosage.cpp:1252:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<double2>::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;
                     ^
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<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int k=0; k<values.size(); k++)
                   ~^~~~~~~~~~~~~~
In file included from idhelp.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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for ( int k = 0 ; k < i->second.size(); k++)
                          ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘std::map<IDField*, std::set<IDValue> > IDHelper::parseQuery(std::__cxx11::string)’:
idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<flist.size(); i++)
                  ~^~~~~~~~~~~~~
idhelp.cpp: In member function ‘bool IDHelper::matchIndividual(IDGroup*, std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int g=0; g<group->values.size(); g++)
                 ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<IDField*, std::set<IDValue> >::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<std::set<IDField*> >::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<IDValue*>::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<bool>::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<IDField*> & jo = jointOrder[j];
                          ^~
idhelp.cpp: In member function ‘std::set<IDGroup*> IDHelper::findAllIndividuals(std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<IDFile>::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<std::set<IDField*> >::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<IDFile>::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<IDField*>::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<IDField*>::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<IDField*> & jf = jointField[j];
                       ^~
idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::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<IDFile>::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<IDField*>::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<IDField*>::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<int>::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<IDField*>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for ( int i=0; i<atoken.size(); i++)
                    ~^~~~~~~~~~~~~~
idhelp.cpp:975:30: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::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<IDGroup*>::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<IDValue*>::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<IDGroup*>::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<IDGroup*>::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<IDValue*>::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<IDGroup*>::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<IDValue*>::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<IDValue*>::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<IDValue*>::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<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
          for (int z=0; z<group->values.size(); z++)
                        ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1189:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::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<IDGroup*>::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<IDValue*>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<ids.size(); i++)
                     ~^~~~~~~~~~~
idhelp.cpp:1424:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::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<IDValue*>::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for ( int i=0; i<targetFields.size(); i++)
                  ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<ids.size(); i++)
                     ~^~~~~~~~~~~
idhelp.cpp:1648:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int i=0; i<rep_field.size(); i++)
                     ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1675:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<rep_field.size(); i++)
                 ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1684:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<rep_field.size(); i++)
                  ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1710:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<rep_field.size(); i++)
                  ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1733:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int f=0; f<targetFields.size(); f++)
                      ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1735:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<rep_field.size(); i++)
                      ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1784:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int f=0; f<targetFields.size(); f++)
                      ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int i=0; i<fstr.size(); i++)
                  ~^~~~~~~~~~~~
idhelp.cpp:1937:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int k=0; k<h.size(); k++)
                  ~^~~~~~~~~
idhelp.cpp:1957:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int f = 0; f<fieldNames.size(); f++)
                    ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:1964:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
        for (int i=0; i<header.size(); i++)
                      ~^~~~~~~~~~~~~~
idhelp.cpp:1986:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, 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<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int k=0; k<tok.size(); k++)
                 ~^~~~~~~~~~~
idhelp.cpp:2030:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int f=0; f<fieldCodes.size(); f++)
                  ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:2070:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int v=0; v<g->values.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<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for (int k=0; k<headers.size(); k++)
                     ~^~~~~~~~~~~~~~~
idhelp.cpp:2168:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  for (int j=0; j<headers[k].size(); j++)
                ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:2201:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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<IDGroup*>::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<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
    for (int j = 0 ; j < group->values.size(); j++ )
                     ~~^~~~~~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> >::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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:24: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:17: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-07-02T13:57:48Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  sensible-utils
Use 'apt autoremove' to remove it.
The following packages will be REMOVED:
  autoconf* automake* autopoint* autotools-dev* binutils-arm-linux-gnueabihf*
  bsdmainutils* cpp-8-arm-linux-gnueabihf* cpp-arm-linux-gnueabihf*
  cross-config* crossbuild-essential-armhf* debhelper* dh-autoreconf*
  dh-strip-nondeterminism* dpkg-cross* dwz* file* g++-8-arm-linux-gnueabihf*
  g++-arm-linux-gnueabihf* gcc-8-arm-linux-gnueabihf*
  gcc-8-arm-linux-gnueabihf-base* gcc-8-base:armhf* gcc-8-cross-base*
  gcc-arm-linux-gnueabihf* gettext* gettext-base* groff-base* intltool-debian*
  libarchive-zip-perl* libasan5:armhf* libasan5-armhf-cross* libatomic1:armhf*
  libatomic1-armhf-cross* libbsd0* libc6:armhf* libc6-armhf-cross*
  libc6-dev:armhf* libc6-dev-armhf-cross* libconfig-auto-perl*
  libconfig-inifiles-perl* libcroco3* libdebian-dpkgcross-perl*
  libfile-homedir-perl* libfile-stripnondeterminism-perl* libfile-which-perl*
  libgcc-8-dev:armhf* libgcc-8-dev-armhf-cross* libgcc1:armhf*
  libgcc1-armhf-cross* libglib2.0-0* libgomp1:armhf* libgomp1-armhf-cross*
  libicu63* libio-string-perl* liblocale-gettext-perl* libmagic-mgc*
  libmagic1* libncurses6* libpipeline1* libsigsegv2* libstdc++-8-dev:armhf*
  libstdc++-8-dev-armhf-cross* libstdc++6:armhf* libstdc++6-armhf-cross*
  libtool* libubsan1:armhf* libubsan1-armhf-cross* libuchardet0*
  libxml-libxml-perl* libxml-namespacesupport-perl* libxml-sax-base-perl*
  libxml-sax-perl* libxml-simple-perl* libxml2* libyaml-perl*
  linux-libc-dev:armhf* linux-libc-dev-armhf-cross* m4* man-db* po-debconf*
  sbuild-build-depends-main-dummy:armhf* ucf* zlib1g:armhf* zlib1g-dev:armhf*
0 upgraded, 0 newly installed, 83 to remove and 0 not upgraded.
After this operation, 231 MB disk space will be freed.
(Reading database ... 18204 files and directories currently installed.)
Removing sbuild-build-depends-main-dummy:armhf (0.invalid.0) ...
Removing crossbuild-essential-armhf (12.6) ...
Removing g++-arm-linux-gnueabihf (4:8.3.0-1) ...
Removing gcc-arm-linux-gnueabihf (4:8.3.0-1) ...
Removing g++-8-arm-linux-gnueabihf (8.3.0-7cross1) ...
Removing gcc-8-arm-linux-gnueabihf (8.3.0-7cross1) ...
Removing binutils-arm-linux-gnueabihf (2.31.1-16) ...
Removing cpp-arm-linux-gnueabihf (4:8.3.0-1) ...
Removing cpp-8-arm-linux-gnueabihf (8.3.0-7cross1) ...
Removing dpkg-cross (2.6.15-3) ...
Removing cross-config (2.6.15-3) ...
Removing libdebian-dpkgcross-perl (2.6.15-3) ...
Removing gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-7cross1) ...
Removing libstdc++-8-dev:armhf (8.3.0-7) ...
Removing libgcc-8-dev:armhf (8.3.0-7) ...
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Removing libasan5:armhf (8.3.0-7) ...
Removing libstdc++6:armhf (8.3.0-7) ...
Removing libstdc++-8-dev-armhf-cross (8.3.0-7cross1) ...
Removing libgcc-8-dev-armhf-cross (8.3.0-7cross1) ...
Removing libubsan1-armhf-cross (8.3.0-7cross1) ...
Removing libasan5-armhf-cross (8.3.0-7cross1) ...
Removing libstdc++6-armhf-cross (8.3.0-7cross1) ...
Removing libatomic1:armhf (8.3.0-7) ...
Removing libatomic1-armhf-cross (8.3.0-7cross1) ...
Removing zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Removing zlib1g:armhf (1:1.2.11.dfsg-1) ...
Removing libc6-dev:armhf (2.28-10) ...
Removing libc6-dev-armhf-cross (2.28-10cross2) ...
Removing libgomp1-armhf-cross (8.3.0-7cross1) ...
Removing libconfig-auto-perl (0.44-1) ...
Removing libconfig-inifiles-perl (3.000001-1) ...
Removing libfile-homedir-perl (1.004-1) ...
Removing libfile-which-perl (1.23-1) ...
Removing libgcc1-armhf-cross (1:8.3.0-7cross1) ...
Removing libgomp1:armhf (8.3.0-7) ...
Removing libxml-simple-perl (2.25-1) ...
Removing libxml-libxml-perl (2.0134+dfsg-1) ...
update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Unregistering 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
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update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::PurePerl with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
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Removing automake (1:1.16.1-4) ...
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Removing dwz (0.12-3) ...
Removing file (1:5.35-4) ...
Removing po-debconf (1.0.21) ...
Removing intltool-debian (0.35.0+20060710.5) ...
Removing gettext (0.19.8.1-9) ...
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Removing groff-base (1.22.4-3) ...
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Removing libarchive-zip-perl (1.64-1) ...
Removing libbsd0:amd64 (0.9.1-2) ...
Removing libc6:armhf (2.28-10) ...
Removing libcroco3:amd64 (0.6.12-3) ...
Removing libgcc1:armhf (1:8.3.0-7) ...
Removing libglib2.0-0:amd64 (2.58.3-2) ...
Removing libxml2:amd64 (2.9.4+dfsg1-7+b3) ...
Removing libicu63:amd64 (63.2-2) ...
Removing libmagic1:amd64 (1:5.35-4) ...
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Removing libncurses6:amd64 (6.1+20181013-2) ...
Removing libpipeline1:amd64 (1.5.1-2) ...
Removing m4 (1.4.18-2) ...
Removing libsigsegv2:amd64 (2.12-2) ...
Removing libuchardet0:amd64 (0.0.6-3) ...
Removing gcc-8-base:armhf (8.3.0-7) ...
Processing triggers for ccache (3.7.1-1) ...
Updating symlinks in /usr/lib/ccache ...
Processing triggers for libc-bin (2.28-10) ...
(Reading database ... 12505 files and directories currently installed.)
Purging configuration files for libglib2.0-0:amd64 (2.58.3-2) ...
Purging configuration files for libmagic1:amd64 (1:5.35-4) ...
Purging configuration files for man-db (2.8.5-2) ...
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Purging configuration files for dpkg-cross (2.6.15-3) ...
Purging configuration files for libdebian-dpkgcross-perl (2.6.15-3) ...
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: n/a
Build-Time: 65
Distribution: unstable-amd64-sbuild
Fail-Stage: build
Foreign Architectures: armhf
Host Architecture: armhf
Install-Time: 13
Job: /home/build/sbuild-setup/repo/pool/main/p/plink/plink_1.07+dfsg-2.dsc
Machine Architecture: amd64
Package: plink
Package-Time: 82
Source-Version: 1.07+dfsg-2
Space: n/a
Status: attempted
Version: 1.07+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-07-02T13:57:48Z
Build needed 00:01:22, no disk space