sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org

+==============================================================================+
| plink 1.07+dfsg-2 (armel)                    Mon, 14 Oct 2019 10:13:55 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-2
Source Version: 1.07+dfsg-2
Distribution: unstable
Machine Architecture: amd64
Host Architecture: armel
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-1337b4c7-2cae-476f-a52b-90d71d361047' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-N2Hs97/resolver-NzMviL' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-14-0814.16.pdiff [4356 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-14-0814.16.pdiff [3192 B]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-14-0814.16.pdiff [4356 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-14-0814.16.pdiff [3192 B]
Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [7904 kB]
Fetched 8106 kB in 2s (4276 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'plink' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/plink.git
Please use:
git clone https://salsa.debian.org/med-team/plink.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 448 kB of source archives.
Get:1 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (dsc) [2077 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (tar) [429 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-2 (diff) [16.7 kB]
Fetched 448 kB in 0s (27.8 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-N2Hs97/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-N2Hs97' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 11), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel
Filtered Build-Depends: debhelper (>= 11), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel
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]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [403 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [495 B]
Fetched 1855 B in 0s (91.4 kB/s)
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-gnueabi
  bsdmainutils cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config
  crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi
  gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel
  gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross
  libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel
  libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl
  libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl
  libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel
  libgcc1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armel
  libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf
  sensible-utils ucf zlib1g:armel zlib1g-dev:armel
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
  | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch
  gcc-9-doc libstdc++6-9-dbg-armel-cross libgcc1-dbg-armel-cross
  libgomp1-dbg-armel-cross libitm1-dbg-armel-cross libatomic1-dbg-armel-cross
  libasan5-dbg-armel-cross liblsan0-dbg-armel-cross libtsan0-dbg-armel-cross
  libubsan1-dbg-armel-cross libquadmath0-dbg-armel-cross manpages-dev flex
  bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel
  manpages-dev:armel libstdc++-9-doc:armel 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:armel 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-gnueabi
  bsdmainutils cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config
  crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi
  gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel
  gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross
  libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel
  libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl
  libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl
  libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel
  libgcc1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armel
  libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross
  libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf
  sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel
  zlib1g-dev:armel
0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
Need to get 62.2 MB of archives.
After this operation, 245 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.7-3 [1300 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b5 [18.9 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-9 [193 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.33-2 [2722 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-8cross1 [193 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-8cross1 [6809 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-8cross1 [188 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-1cross7 [1139 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armel-cross all 1:9.2.1-8cross1 [39.0 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 9.2.1-8cross1 [74.9 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 9.2.1-8cross1 [8932 B]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-8cross1 [340 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 9.2.1-8cross1 [376 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 9.2.1-8cross1 [110 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-8cross1 [640 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-8cross1 [7143 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.2.9-2cross7 [1312 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-1cross7 [2155 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-8cross1 [1705 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-8cross1 [7387 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.0-1 [23.3 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.0-1 [14.3 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-1 [81.8 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.6.1 [172 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.1-1 [1317 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190803-1 [102 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.6.1 [993 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main armel libgcc1 armel 1:9.2.1-9 [39.0 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-2 [2349 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-9 [347 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 9.2.1-9 [9092 B]
Get:79 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.2.17-1+b1 [1232 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-2 [2196 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 9.2.1-9 [77.1 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 9.2.1-9 [414 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 9.2.1-9 [111 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-9 [641 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-9 [1737 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-1+b1 [84.7 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-1+b1 [204 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libxml-sax-base-perl (1.09-1) ...
Setting up libio-string-perl (1.08-3) ...
Setting up autotools-dev (20180224.1) ...
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Setting up libc6-armel-cross (2.29-1cross7) ...
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Setting up liblocale-gettext-perl (1.07-3+b5) ...
Setting up gcc-9-base:armel (9.2.1-9) ...
Setting up libfile-stripnondeterminism-perl (1.6.0-1) ...
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Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-2) ...
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Setting up libgcc1-armel-cross (1:9.2.1-8cross1) ...
Setting up libasan5-armel-cross (9.2.1-8cross1) ...
Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ...
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 (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up libstdc++6-armel-cross (9.2.1-8cross1) ...
Setting up man-db (2.8.7-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+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 intltool-debian (0.35.0+20060710.5) ...
Setting up libubsan1-armel-cross (9.2.1-8cross1) ...
Setting up libgcc-9-dev-armel-cross (9.2.1-8cross1) ...
Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ...
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
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Setting up libstdc++-9-dev-armel-cross (9.2.1-8cross1) ...
Setting up gcc-9-arm-linux-gnueabi (9.2.1-8cross1) ...
Setting up g++-9-arm-linux-gnueabi (9.2.1-8cross1) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ...
Setting up libconfig-auto-perl (0.44-1) ...
Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ...
Setting up libdebian-dpkgcross-perl (2.6.15-3) ...
Setting up dpkg-cross (2.6.15-3) ...
Setting up crossbuild-essential-armel (12.8) ...
Setting up libgcc1:armel (1:9.2.1-9) ...
Setting up libc6:armel (2.29-2) ...
Setting up libc6-dev:armel (2.29-2) ...
Setting up libstdc++6:armel (9.2.1-9) ...
Setting up debhelper (12.6.1) ...
Setting up zlib1g:armel (1:1.2.11.dfsg-1+b1) ...
Setting up libgomp1:armel (9.2.1-9) ...
Setting up dh-autoreconf (19) ...
Setting up libasan5:armel (9.2.1-9) ...
Setting up libatomic1:armel (9.2.1-9) ...
Setting up libubsan1:armel (9.2.1-9) ...
Setting up dh-strip-nondeterminism (1.6.0-1) ...
Setting up zlib1g-dev:armel (1:1.2.11.dfsg-1+b1) ...
Setting up libgcc-9-dev:armel (9.2.1-9) ...
Setting up libstdc++-9-dev:armel (9.2.1-9) ...
Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2) ...

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

Arch check ok (armel included in any)

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

Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64)
Toolchain package versions: binutils_2.33-2 dpkg-dev_1.19.7 g++-8_8.3.0-23 g++-9_9.2.1-9 gcc-8_8.3.0-23 gcc-9_9.2.1-9 libc6-dev_2.29-2 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-9 libstdc++-9-dev-armel-cross_9.2.1-8cross1 libstdc++6_9.2.1-9 libstdc++6-armel-cross_9.2.1-8cross1 linux-libc-dev_5.2.17-1+b1
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.33-2 binutils-arm-linux-gnueabi_2.33-2 binutils-common_2.33-2 binutils-x86-64-linux-gnu_2.33-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-23 cpp-9_9.2.1-9 cpp-9-arm-linux-gnueabi_9.2.1-8cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.6.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-23 g++-9_9.2.1-9 g++-9-arm-linux-gnueabi_9.2.1-8cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-23 gcc-8-base_8.3.0-23 gcc-9_9.2.1-9 gcc-9-arm-linux-gnueabi_9.2.1-8cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-8cross1 gcc-9-base_9.2.1-9 gcc-9-cross-base_9.2.1-8cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.22+b1 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-9 libasan5-armel-cross_9.2.1-8cross1 libatomic1_9.2.1-9 libatomic1-armel-cross_9.2.1-8cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33-2 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2 libc-dev-bin_2.29-2 libc6_2.29-2 libc6-armel-cross_2.29-1cross7 libc6-dev_2.29-2 libc6-dev-armel-cross_2.29-1cross7 libcap-ng0_0.7.9-2+b1 libcc1-0_9.2.1-9 libcom-err2_1.45.4-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.6.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-23 libgcc-9-dev_9.2.1-9 libgcc-9-dev-armel-cross_9.2.1-8cross1 libgcc1_1:9.2.1-9 libgcc1-armel-cross_1:9.2.1-8cross1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.1-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-5 libgomp1_9.2.1-9 libgomp1-armel-cross_9.2.1-8cross1 libgpg-error0_1.36-7 libhogweed4_3.5.1+really3.4.1-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl21_0.21-2 libitm1_9.2.1-9 liblocale-gettext-perl_1.07-3+b5 liblsan0_9.2.1-9 liblz4-1_1.9.1-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-23 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.5.1+really3.4.1-1 libp11-kit0_0.23.17-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-6 libpipeline1_1.5.1-2 libquadmath0_9.2.1-9 libseccomp2_2.4.1-2 libselinux1_2.9-2+b2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.4-1 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-9 libstdc++-9-dev-armel-cross_9.2.1-8cross1 libstdc++6_9.2.1-9 libstdc++6-armel-cross_9.2.1-8cross1 libsub-override-perl_0.09-2 libsystemd0_242-7 libtasn1-6_4.14-3 libtinfo6_6.1+20190803-1 libtool_2.4.6-11 libtsan0_9.2.1-9 libubsan1_9.2.1-9 libubsan1-armel-cross_9.2.1-8cross1 libuchardet0_0.0.6-3 libudev1_242-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.2.17-1+b1 linux-libc-dev-armel-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-6 perl-base_5.30.0-6 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-6 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 zlib1g-dev_1:1.2.11.dfsg-1+b1

+------------------------------------------------------------------------------+
| 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
CONFIG_SITE=/etc/dpkg-cross/cross-config.armel
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1003
SCHROOT_GROUP=helmut
SCHROOT_SESSION_ID=unstable-amd64-sbuild-1337b4c7-2cae-476f-a52b-90d71d361047
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
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-gnueabi 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 armel
 fakeroot debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j1 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
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]
   73 |        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]
  252 |       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]
  196 |     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]
  763 |       par::make_founders &&
      |       ~~~~~~~~~~~~~~~~~~~^~
  764 |       !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]
 2106 |   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]
 2359 |   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]
 2362 |   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]
 2366 |     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 options.cpp
In file included from options.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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 input.cpp
In file included from input.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readData()’:
input.cpp:516:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  516 |        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]
  521 |        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]
  545 |    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]
  579 |     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]
  595 |       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]
  611 |   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]
  631 |       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]
  695 |       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]
  787 |   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]
  817 |       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]
  821 |        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]
  897 |   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]
  927 |    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]
  961 |       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]
  965 |       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]
 1037 |     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]
 1043 |   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]
 1064 |       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]
 1208 |       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]
 1232 |   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]
 1256 |       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]
 1261 |      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]
 1335 |   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]
 1374 |       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]
 1519 |    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]
 1538 |       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]
 1572 |   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]
 1599 |       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]
 1602 |    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]
 1745 |    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]
 1764 |       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]
 1792 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readMapFile(std::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]
 2116 |   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]
 2172 |       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]
 2200 |       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]
 2210 |       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]
 2215 |   if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
      |                                               ~~~~~~~~~~^~~~~~~~~~~~~~
input.cpp:2225:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2225 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readFamFile(std::string)’:
input.cpp:2389:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2389 |     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]
 2397 |   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]
 2419 |       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]
 2453 |       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]
 2471 |   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]
 2732 |       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]
   91 |    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 binput.cpp
In file included from binput.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
binput.cpp: In member function ‘void Plink::readBinData()’:
binput.cpp:126:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  126 |   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]
  157 |       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]
  176 |       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]
  186 |       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]
  261 |    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]
  339 |        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]
  351 |     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]
  398 |       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 tinput.cpp
In file included from tinput.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
tinput.cpp: In member function ‘void Plink::readTransposedData()’:
tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |   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]
  218 |       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]
  246 |       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]
  256 |       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]
  261 |   if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
      |                                               ~~~~~~~~~~^~~~~~~~~~~~~~
tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  271 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  309 |       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]
  591 |    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]
  603 |       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 genome.cpp
In file included from genome.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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]
   99 |    int geno_nm = 0;
      |        ^~~~~~~
genome.cpp:81:14: warning: unused variable ‘tothet’ [-Wunused-variable]
   81 |       double tothet = 0;
      |              ^~~~~~
genome.cpp: In member function ‘void Plink::calcFst()’:
genome.cpp:391:14: warning: unused variable ‘ht’ [-Wunused-variable]
  391 |       double ht = 2 * locus[l]->freq * ( 1 - locus[l]->freq );
      |              ^~
genome.cpp: In member function ‘Z Plink::calcGenomeIBD(Individual*, Individual*, Z)’:
genome.cpp:843:10: warning: unused variable ‘e10’ [-Wunused-variable]
  843 |   double e10 = E10*S;
      |          ^~~
genome.cpp:844:10: warning: unused variable ‘e20’ [-Wunused-variable]
  844 |   double e20 = E20*S;
      |          ^~~
genome.cpp:848:10: warning: unused variable ‘e21’ [-Wunused-variable]
  848 |   double e21 = E21*S;
      |          ^~~
genome.cpp: In member function ‘void Plink::displayGenomeWideInfo()’:
genome.cpp:1067:23: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 1067 |  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]
 1227 |   for (int i=0;i<chrs.size();i++)
      |                ~^~~~~~~~~~~~
genome.cpp:1189:7: warning: unused variable ‘win_end’ [-Wunused-variable]
 1189 |   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 helper.cpp
In file included from helper.h:24,
                 from helper.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::string display(std::vector<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]
   58 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
helper.cpp: In function ‘std::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]
   66 |   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]
   76 |   for (int i=0; i< m.size(); i++)
      |                 ~^~~~~~~~~~
helper.cpp:79:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |       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]
   90 |   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]
  100 |   for (int i=0; i< m.size(); i++)
      |                 ~^~~~~~~~~~
helper.cpp: In member function ‘void CArgs::fromPriorLog(std::string)’:
helper.cpp:193:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |       for (int t=0; t<tokens.size(); t++)
      |                     ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > CArgs::value(std::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]
  267 |      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]
  277 |   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::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]
  306 |   for (int i=0 ; i < s.length() ; i++)
      |                  ~~^~~~~~~~~~~~
helper.cpp:307:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  307 |     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]
  309 |  if (i == s.length()-1) t += s[i];
      |      ~~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> parse2int(std::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]
  323 |   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]
  461 |   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]
  595 |       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]
  611 |       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]
  659 |       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]
  664 |       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]
  709 |   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]
  729 |   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]
  775 |   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]
  795 |   for (int s = 0 ; s < snps.size() ; s++)
      |                    ~~^~~~~~~~~~~~~
helper.cpp: In function ‘std::string chromosomeName(int)’:
helper.cpp:952:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  952 |   if ( c < 0 || c >= par::chr_code.size() )
      |                 ~~^~~~~~~~~~~~~~~~~~~~~~~
helper.cpp: In function ‘int getMarkerChromosome(Plink&, std::string)’:
helper.cpp:959:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  959 |   for (int i=0;i<P.locus.size();i++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘int getMarkerNumber(Plink&, std::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]
  966 |   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]
  973 |   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]
  989 |   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]
 1040 |   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]
 1172 |   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]
 1264 |       if (sample[i]->fid.length() > par::pp_maxfid)
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1267 |       if (sample[i]->iid.length() > par::pp_maxiid)
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1273 |     if (locus[l]->name.length() > par::pp_maxsnp)
      |         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<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]
 1389 |    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]
 1391 |        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]
 2204 |        int i = 0;
      |            ^
helper.cpp: In member function ‘void Plink::filterOnCovariate()’:
helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2455 |   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]
 2462 |       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]
 2491 |   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]
 2510 |   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]
 2530 |   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]
 2549 |   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]
 2568 |   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]
 2587 |   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]
 2606 |   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]
 2638 |   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]
 2671 |       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]
 2722 |   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]
 2756 |       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]
 2935 |   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]
 2959 |   if ( input.size() != P.nl_all )
      |        ~~~~~~~~~~~~~^~~~~~~~~~~
helper.cpp: In function ‘std::map<std::__cxx11::basic_string<char>, std::set<Range> > readRange(std::string)’:
helper.cpp:3097:20: warning: unused variable ‘s’ [-Wunused-variable]
 3097 |       set<Range> * s;
      |                    ^
helper.cpp: In function ‘void makeScaffold(Plink&)’:
helper.cpp:3324:9: warning: unused variable ‘last’ [-Wunused-variable]
 3324 |     int last = -1;
      |         ^~~~
helper.cpp:3328:9: warning: unused variable ‘thisChromosome’ [-Wunused-variable]
 3328 |     int thisChromosome = P.locus[0]->chr;
      |         ^~~~~~~~~~~~~~
helper.cpp:3329:9: warning: unused variable ‘nextChromosome’ [-Wunused-variable]
 3329 |     int nextChromosome;
      |         ^~~~~~~~~~~~~~
helper.cpp: In member function ‘std::string CArgs::value(std::string)’:
helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type]
  218 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘int CArgs::value_int(std::string)’:
helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type]
  231 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘long unsigned int CArgs::value_lui(std::string)’:
helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type]
  243 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘double CArgs::value_double(std::string)’:
helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type]
  255 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘int getInt(std::string, std::string)’:
helper.cpp:378:48: warning: control reaches end of non-void function [-Wreturn-type]
  378 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘long unsigned int getLongUnsignedInt(std::string, std::string)’:
helper.cpp:391:48: warning: control reaches end of non-void function [-Wreturn-type]
  391 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘double getDouble(std::string, std::string)’:
helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type]
  404 |       error("Not valid numeric argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘void makeScaffold(Plink&)’:
helper.cpp:3342:12: warning: ‘*((void*)& ci +4)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3342 |      CInfo ci;
      |            ^~
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
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]
   73 |        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]
  458 |   int m,l,iter,i,k;
      |                  ^
stats.cpp: In function ‘bool svd(matrix_t&, vector_t&, matrix_t&)’:
stats.cpp:813:16: warning: unused variable ‘eps’ [-Wunused-variable]
  813 |   const double eps = 1e-12;
      |                ^~~
stats.cpp:818:7: warning: unused variable ‘r’ [-Wunused-variable]
  818 |   int r = u.size();
      |       ^
stats.cpp: In function ‘std::vector<std::vector<double> > msqrt(std::vector<std::vector<double> >&)’:
stats.cpp:906:16: warning: unused variable ‘eps’ [-Wunused-variable]
  906 |   const double eps = 1e-12;
      |                ^~~
stats.cpp: In function ‘int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)’:
stats.cpp:1477:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1477 |  for (int c = 0 ; c < keep.size(); c++)
      |                   ~~^~~~~~~~~~~~~
stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1483 |       for (int c = 0 ; c < keep.size(); c++)
      |                        ~~^~~~~~~~~~~~~
stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1515 |     for (int c = 0 ; c < keep.size(); c++)
      |                      ~~^~~~~~~~~~~~~
stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1521 |   for (int c = 0 ; c < keep.size(); c++)
      |                    ~~^~~~~~~~~~~~~
stats.cpp: In function ‘matrix_t vec2diag(vector_t&)’:
stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1531 |   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 filters.cpp
In file included from filters.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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]
   95 |    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]
  123 |    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]
  132 |        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]
  155 |    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]
  163 |        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]
  198 |    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]
  273 |        for (int i=0; i<tokens.size(); i++)
      |                      ~^~~~~~~~~~~~~~
filters.cpp:249:14: warning: unused variable ‘freq’ [-Wunused-variable]
  249 |       double freq;
      |              ^~~~
filters.cpp:250:11: warning: unused variable ‘nm’ [-Wunused-variable]
  250 |       int nm;
      |           ^~
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]
  591 |       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]
  611 |       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]
  739 |       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]
  762 |    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]
 1078 |        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]
 1091 |        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]
 1143 |       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]
 1165 |        for ( int i=0; i<sample.size(); i++)
      |                       ~^~~~~~~~~~~~~~
filters.cpp:1257:7: warning: unused variable ‘tmp’ [-Wunused-variable]
 1257 |   int tmp = deleteSNPs(del);
      |       ^~~
filters.cpp: In member function ‘void Plink::thinSNPs()’:
filters.cpp:1277:7: warning: unused variable ‘x’ [-Wunused-variable]
 1277 |   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 locus.cpp
In file included from locus.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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 multi.cpp
In file included from multi.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
multi.cpp: In member function ‘std::vector<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]
  295 |       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]
  304 |       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]
  357 |        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]
  372 |    for (int i=0; i<pos.size()-1; i++)
      |                  ~^~~~~~~~~~~~~
multi.cpp:154:8: warning: unused variable ‘is0zero’ [-Wunused-variable]
  154 |   bool is0zero = IBDg.z0 < EPS ? true : false;
      |        ^~~~~~~
multi.cpp:155:8: warning: unused variable ‘is1zero’ [-Wunused-variable]
  155 |   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 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
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]
   73 |        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]
  272 |     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]
  452 |     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]
  511 |     for (int i=0;i<val.size();i++)
      |                  ~^~~~~~~~~~~
cluster.cpp:492:8: warning: unused variable ‘size’ [-Wunused-variable]
  492 |    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]
  626 |    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]
  648 |        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]
  651 |     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]
  784 |       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]
  786 |    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]
  919 |  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]
  954 |       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]
  955 |  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]
  975 |    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]
  976 |      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]
  990 |    (( 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]
 1038 |    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]
 1041 |    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]
 1049 |    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]
 1050 |      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]
 1060 |    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]
 1061 |      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]
 1107 |    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]
 1110 |        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]
 1133 |    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]
 1163 |       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]
 1169 |    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]
 1203 |   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]
 1204 |     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]
 1228 |   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]
 1229 |     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]
 1254 |   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]
 1255 |     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]
 1272 |   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]
 1276 |   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]
 1290 |   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]
 1291 |     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]
 1643 |   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]
 1661 |       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]
 1664 |    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 mds.cpp
In file included from mds.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mds.cpp: In member function ‘void Plink::generateMDS()’:
mds.cpp:190:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  190 |   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]
  191 |     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]
  279 |   if ( elist.size() != par::cluster_mds_dim )
      |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
mds.cpp:242:8: warning: unused variable ‘flag’ [-Wunused-variable]
  242 |   bool flag = svd(D,eigenvalue,eigenvector);
      |        ^~~~
g++ -Wall -g  -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
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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::displayGenomePV()’:
output.cpp:84:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |   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]
   86 |       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]
   89 |    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]
  402 |   vector<Locus*>::iterator loc1 = locus.begin()+m1;
      |                            ^~~~
output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable]
  403 |   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]
  520 |       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]
  526 |        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]
  553 |       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]
  788 |   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]
 2200 |   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]
 2322 |   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]
 2367 |   for (int i=0; i < setname.size();i++)
      |                 ~~^~~~~~~~~~~~~~~~
output.cpp:2380:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2380 |       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]
 2409 |   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]
 2412 |       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]
  144 |    << 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]
  145 |    << 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]
   69 |   << 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 informative.cpp
In file included from informative.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
informative.cpp: In member function ‘int Plink::readInformative()’:
informative.cpp:80:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   80 |   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]
  102 |       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]
  105 |    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 assoc.cpp
In file included from helper.h:24,
                 from assoc.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from assoc.cpp:29:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  395 |    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]
  741 |      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]
  744 |   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]
  785 |       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]
  788 |    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]
 1536 |       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:1109:61: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1109 |      pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) );
      |                                                        ~~~~~^~~~~~~~~~
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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
epi.cpp: In member function ‘void Plink::calcEpistasis()’:
epi.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  146 |       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]
  154 |    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]
  161 |    for (int e=0;e<snpset[0].size();e++)
      |                 ~^~~~~~~~~~~~~~~~~
epi.cpp:438:12: warning: unused variable ‘zero’ [-Wunused-variable]
  438 |     double zero = 0;
      |            ^~~~
epi.cpp:701:11: warning: unused variable ‘c’ [-Wunused-variable]
  701 |       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 prephap.cpp
In file included from prephap.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from prephap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  226 |        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]
  283 |     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]
  412 |    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]
  416 |        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]
  420 |        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]
  470 |    for (int s=0;s<S.size();s++)
      |                 ~^~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::makeSlidingWindow(std::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]
  533 |   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]
  560 |   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 phase.cpp
In file included from phase.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from phase.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
  373 |        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]
  472 |   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]
  678 |         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]
 1187 |       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]
 1238 |    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]
 1280 |        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]
 1299 |    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]
 1575 |     for ( int z = 0 ; z < pp[i].size() ; z++ )
      |                       ~~^~~~~~~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::prunePhase(int)’:
phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1829 |   for (int z=0; z < hap1[i].size(); z++)
      |                 ~~^~~~~~~~~~~~~~~~
phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1843 |       for (int z=0; z < new_pp.size(); z++)
      |                     ~~^~~~~~~~~~~~~~~
phase.cpp: In member function ‘double HaploPhase::dosage(int, std::set<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]
 1888 |       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 trio.cpp
In file included from trio.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
trio.cpp: In function ‘void addPerson(Family*, Individual*)’:
trio.cpp:91:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   91 |   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]
  258 |        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]
  272 |        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]
  335 |   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]
  342 |        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]
  350 |        for ( int k=0; k<(*f)->kid.size(); k++)
      |                       ~^~~~~~~~~~~~~~~~~
trio.cpp: In member function ‘void Plink::checkMendel()’:
trio.cpp:469:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  469 |   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]
  474 |   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]
  492 |       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]
  504 |    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]
  871 |       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]
  882 |       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]
  895 |        for (int c=0; c<kid.size(); c++)
      |                      ~^~~~~~~~~~~
trio.cpp:931:6: warning: unused variable ‘tmp’ [-Wunused-variable]
  931 |  int tmp = deleteSNPs(mendel_locus);
      |      ^~~
trio.cpp:936:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  936 |       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]
  943 |        for (int c=0; c<family[f]->kid.size(); c++)
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
trio.cpp:962:6: warning: unused variable ‘tmp’ [-Wunused-variable]
  962 |  int tmp = deleteIndividuals(indel);
      |      ^~~
trio.cpp: In member function ‘void Plink::pseudoCaseControl()’:
trio.cpp:1038:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1038 |   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]
 1048 |       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]
 1236 |    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]
 1245 |    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 tdt.cpp
In file included from tdt.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
tdt.cpp: In member function ‘void Plink::perm_testTDT(Perm&)’:
tdt.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |    for (int i=0; i<klist[k]->person.size(); i++)
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:96:16: warning: unused variable ‘person’ [-Wunused-variable]
   96 |   Individual * person = klist[k]->person[i];
      |                ^~~~~~
tdt.cpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  132 |       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]
  144 |    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]
  210 |    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]
  234 |       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]
  327 |      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]
  330 |   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]
  412 |       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]
  415 |    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]
  522 |       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]
  557 |    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]
  668 |    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]
  776 |    for (int f=0; f<family.size(); f++)
      |                  ~^~~~~~~~~~~~~~
tdt.cpp:936:41: warning: ‘zt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  936 |     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 sharing.cpp
In file included from perm.h:17,
                 from sharing.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
sharing.cpp: In member function ‘void Plink::perm_sharingIBSTest(Perm&)’:
sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  102 |   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 genepi.cpp
In file included from genepi.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
genepi.cpp: In function ‘double C(int, double, double)’:
genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type]
   78 | }
      | ^
genepi.cpp: In function ‘long double pillai(int, int, int, double)’:
genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type]
  169 | }
      | ^
genepi.cpp: In member function ‘void Plink::driverSCREEPI()’:
genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  334 |   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]
  489 |      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]
  497 |      for (int l=0; l<P.snpset[s2].size(); l++)
      |                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:506:10: warning: unused variable ‘n12’ [-Wunused-variable]
  506 |      int n12 = n1 + n2;
      |          ^~~
genepi.cpp:507:10: warning: unused variable ‘ne’ [-Wunused-variable]
  507 |      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]
 1025 |      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]
 1033 |      for (int l=0; l<P.snpset[s2].size(); l++)
      |                    ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:1043:10: warning: unused variable ‘n12’ [-Wunused-variable]
 1043 |      int n12 = n1 + n2;
      |          ^~~
genepi.cpp:1044:10: warning: unused variable ‘ne’ [-Wunused-variable]
 1044 |      int ne = n1 < n2 ? n1 : n2;// ne = min(p,q)
      |          ^~
genepi.cpp:1064:10: warning: unused variable ‘nind’ [-Wunused-variable]
 1064 |      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]
 1198 |   bool casewise_deletion = false;
      |        ^~~~~~~~~~~~~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:855:84: warning: ‘cancor1_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  855 |        gene2[i] += (-1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp];
      |                                                                                    ^
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 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]
   73 |        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]
  252 |       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]
   37 |   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]
   52 |       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]
   59 |    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]
   62 |    if (par::set_max==-1 || par::set_max > snpset[i].size() )
      |                            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneSets(Plink&)’:
sets.cpp:99:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   99 |   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]
  129 |   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]
  176 |       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]
  216 |   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]
  218 |       for (int j=0; j < snpset[i].size(); j++)
      |                     ~~^~~~~~~~~~~~~~~~~~
sets.cpp:236:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |   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]
  237 |     for (int j=0; j < snpset[i].size(); j++)
      |                   ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::makeLDSets()’:
sets.cpp:317:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  317 |   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]
  323 |       for (int j=0; j < snpset[i].size(); j++)
      |                     ~~^~~~~~~~~~~~~~~~~~
sets.cpp:329:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  329 |       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]
  332 |    for (int k=j+1; k < snpset[i].size(); k++)
      |                    ~~^~~~~~~~~~~~~~~~~~
sets.cpp:367:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |       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]
  370 |    for (int j=0; j < snpset[i].size(); j++)
      |                  ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::initialiseSetMapping()’:
sets.cpp:412:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  412 |   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]
  413 |     for (int j=0; j < snpset[i].size(); j++)
      |                   ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::empiricalSetPValues()’:
sets.cpp:618:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  618 |       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]
  619 |  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]
  631 |       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]
  632 |  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]
  642 |       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]
  643 |  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]
  703 |   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]
  713 |       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]
  905 |   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]
  975 |    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]
 1042 |   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 perm.cpp
In file included from perm.h:17,
                 from perm.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::permuteInCluster()’:
perm.cpp:144:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |   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]
  145 |     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]
  187 |   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]
  199 |   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]
  273 |      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 mh.cpp
In file included from perm.h:17,
                 from mh.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mh.cpp: In member function ‘std::vector<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]
  747 |   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]
 1249 |   for (int i=0; i<X.size(); i++)
      |                 ~^~~~~~~~~
mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type]
 1312 | }
      | ^
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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::preGeneDrop()’:
genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   64 |   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]
  340 |   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 gxe.cpp
In file included from helper.h:24,
                 from gxe.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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 merge.cpp
In file included from merge.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
merge.cpp: In member function ‘void Plink::mergeData()’:
merge.cpp:333:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  333 |   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]
  377 |   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]
  395 |   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]
  403 |        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]
  426 |       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]
  722 |    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]
  733 |       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]
  784 |     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]
  830 |       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]
  842 |    for (int i=0; i<sample.size(); i++)
      |                  ~^~~~~~~~~~~~~~
merge.cpp: In member function ‘bool Plink::reconcileMerge(int, int, std::string, std::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]
 1103 |   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 hotel.cpp
In file included from hotel.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
hotel.cpp: In member function ‘void Plink::perm_testHotel(Perm&)’:
hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   77 |     if (!sample[i]->missing)
      |        ^
hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  173 |   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 multiple.cpp
In file included from helper.h:24,
                 from multiple.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
multiple.cpp: In member function ‘void Plink::multcomp(std::vector<double>&, std::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]
   85 |   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]
  131 |   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 haploCC.cpp
In file included from haploCC.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from haploCC.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
   48 |        for (int z = 0 ; z < hap1[i].size(); z++)
      |                         ~~^~~~~~~~~~~~~~~~
haploCC.cpp:62:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   62 |     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]
   79 |        for (int z = 0 ; z < hap1[i].size(); z++)
      |                         ~~^~~~~~~~~~~~~~~~
haploCC.cpp:93:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   93 |     if ( ! ( haploid || X && person->sex ) )
      |                         ~~^~~~~~~~~~~~~~
haploCC.cpp:268:14: warning: unused variable ‘p’ [-Wunused-variable]
  268 |       double p = ( n1 * p1 + n2 * p2 ) / ( n1 + n2 );
      |              ^
haploCC.cpp: In member function ‘void HaploPhase::haplotypicWeightedCC()’:
haploCC.cpp:340:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  340 |         for (int z = 0 ; z < hap1[i].size(); z++)
      |                          ~~^~~~~~~~~~~~~~~~
haploCC.cpp:357:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  357 |     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]
  375 |         for (int z = 0 ; z < hap1[i].size(); z++)
      |                          ~~^~~~~~~~~~~~~~~~
haploCC.cpp:392:28: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  392 |      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 haploTDT.cpp
In file included from haploTDT.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from haploTDT.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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 poo.cpp
In file included from poo.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘void Plink::perm_testTDT_POO(Perm&)’:
poo.cpp:93:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   93 |       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]
  195 |       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]
  198 |    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]
  293 |       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]
  328 |    for (int c=0; c<kid.size(); c++)
      |                  ~^~~~~~~~~~~
poo.cpp:239:10: warning: unused variable ‘zt’ [-Wunused-variable]
  239 |   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 webcheck.cpp
In file included from helper.h:24,
                 from webcheck.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
webcheck.cpp: In member function ‘void Plink::webcheck(CArgs&)’:
webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  117 |   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]
  130 |    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]
  146 |    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]
  180 |    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]
  218 |   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 qfam.cpp
In file included from helper.h:24,
                 from qfam.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
qfam.cpp: In function ‘void scoreBetween(Plink&, int)’:
qfam.cpp:82:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   82 |        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]
   89 |        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]
   97 |        for ( int k=0; k<(*f)->kid.size(); k++)
      |                       ~^~~~~~~~~~~~~~~~~
qfam.cpp: In member function ‘void Plink::perm_testQTDT(Perm&)’:
qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int i=0; i < family.size(); i++)
      |                 ~~^~~~~~~~~~~~~~~
qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |   for (int f = 0 ; f < family.size() ; f++)
      |                    ~~^~~~~~~~~~~~~~~
qfam.cpp: In member function ‘vector_t Plink::calcQTDT(std::vector<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]
  505 |        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]
  648 |   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]
  657 |   for (int f=0; f<pbetween.size(); f++)
      |                 ~^~~~~~~~~~~~~~~~
qfam.cpp:639:10: warning: unused variable ‘tc’ [-Wunused-variable]
  639 |      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 linear.cpp
In file included from helper.h:24,
                 from linear.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
linear.cpp: In member function ‘virtual void LinearModel::pruneY()’:
linear.cpp:50:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   50 |   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]
  734 |   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]
  100 |     indxr[i]=irow;
linear.cpp:108:7: warning: ‘icol’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  108 |       if (ll != 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 bmerge.cpp
In file included from bmerge.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
bmerge.cpp: In member function ‘void Plink::mergeBinaryData()’:
bmerge.cpp:90:16: warning: variable ‘inc’ set but not used [-Wunused-but-set-variable]
   90 |       long int inc;
      |                ^~~
bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  357 |   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]
  390 |   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]
  409 |   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]
  417 |        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]
  440 |       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]
  549 |       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]
  697 |       while (s<locus2.size()) // for all SNPs in second file
      |              ~^~~~~~~~~~~~~~
bmerge.cpp:692:14: warning: unused variable ‘snp’ [-Wunused-variable]
  692 |       CSNP * snp;
      |              ^~~
bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  839 |     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]
  871 |       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]
  883 |    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 parse.cpp
In file included from parse.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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
   80 | 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 -c mishap.cpp
In file included from mishap.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from mishap.cpp:20:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  209 |         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]
  236 |         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]
  349 |        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]
  373 |        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 legacy.cpp
In file included from helper.h:24,
                 from legacy.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
legacy.cpp: In member function ‘void Plink::calcRegression(int)’:
legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  368 |   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]
  377 |       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]
  381 |       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]
  384 |    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]
  390 |       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]
  395 |       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]
  415 |   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]
  424 |   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]
  460 |       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]
  461 |  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]
  462 |    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]
  467 |       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]
  480 |       for (int i=0; i<pair1.size(); i++)
      |                     ~^~~~~~~~~~~~~
legacy.cpp: In member function ‘void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)’:
legacy.cpp:206:51: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  206 |         << (double)( locus[start]->bp - locus[last]->bp ) / 1000.0
      |                                                   ^
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 homozyg.cpp
In file included from helper.h:24,
                 from homozyg.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
homozyg.cpp: In function ‘void displayPoolVerbose(Plink&, Pool*, std::ofstream&)’:
homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  673 |   for (int i=0; i < plist.size(); i++)
      |                 ~~^~~~~~~~~~~~~~
homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  695 |   for (int i=0; i < plist.size(); i++)
      |                 ~~^~~~~~~~~~~~~~
homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  722 |       for (int i=0; i < plist.size(); i++)
      |                     ~~^~~~~~~~~~~~~~
homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  756 |       for (int i=0; i < plist.size(); i++)
      |                     ~~^~~~~~~~~~~~~~
homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  773 |       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]
  861 |    for (int i=0; i < plist.size(); i++)
      |                  ~~^~~~~~~~~~~~~~
homozyg.cpp: In member function ‘void Plink::summariseHomoRuns()’:
homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1134 |       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]
 1178 |    if ( thispool->segs.size() >= par::pool_size_min )
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1331 |       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]
 1437 |    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]
 1441 |     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]
 1461 |    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]
 2155 |  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 segment.cpp
In file included from helper.h:24,
                 from segment.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
segment.cpp:871:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  871 |  if (!ibd)
      |  ^~
segment.cpp:875:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  875 |    SIBS << setw(10) << original[l]  << " "
      |    ^~~~
segment.cpp: In member function ‘void Plink::testGenomeIBDByCovariate(Perm&)’:
segment.cpp:954:15: warning: unused variable ‘p1’ [-Wunused-variable]
  954 |  Individual * p1 = sample[i1];
      |               ^~
segment.cpp:955:15: warning: unused variable ‘p2’ [-Wunused-variable]
  955 |  Individual * p2 = sample[i2];
      |               ^~
segment.cpp:1027:19: warning: unused variable ‘p1’ [-Wunused-variable]
 1027 |      Individual * p1 = sample[i1];
      |                   ^~
segment.cpp:1028:19: warning: unused variable ‘p2’ [-Wunused-variable]
 1028 |      Individual * p2 = sample[i2];
      |                   ^~
segment.cpp:950:7: warning: unused variable ‘c’ [-Wunused-variable]
  950 |   int c=0;
      |       ^
segment.cpp: In member function ‘void Plink::summaryIBD()’:
segment.cpp:1529:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1529 |   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]
 1855 |    indivPair p = ic->first;
      |              ^
segment.cpp: In member function ‘void Plink::displaySegmentsLong()’:
segment.cpp:2003:12: warning: unused variable ‘nseg’ [-Wunused-variable]
 2003 |        int nseg = smap.size();
      |            ^~~~
segment.cpp: In member function ‘void Plink::displaySegmentsBED()’:
segment.cpp:2378:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2378 |    else if ( par::cnv_col = 1 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2380:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2380 |    else if ( par::cnv_col = 2 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2382:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2382 |    else if ( par::cnv_col = 3 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2412:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2412 |    else if ( par::cnv_col = 1 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2414:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2414 |    else if ( par::cnv_col = 2 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2416:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2416 |    else if ( par::cnv_col = 3 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2443:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2443 |    else if ( par::cnv_col = 1 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2445:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2445 |    else if ( par::cnv_col = 2 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2447:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2447 |    else if ( par::cnv_col = 3 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2474:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2474 |    else if ( par::cnv_col = 1 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2476:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2476 |    else if ( par::cnv_col = 2 )
      |              ~~~~~~~~~~~~~^~~
segment.cpp:2478:27: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2478 |    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 model.cpp
In file included from model.cpp:15:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from model.cpp:17:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  132 |   if ( include.size() != P->n )
      |        ~~~~~~~~~~~~~~~^~~~~~~
model.cpp: In member function ‘void Model::buildDesignMatrix()’:
model.cpp:354:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  354 |       for (int i=0; i< par::parameter_list.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:367:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |       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]
  374 |    for ( int j = 0 ; j < par::parameter_list.size() ; j++)
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp: In member function ‘bool Model::checkVIF()’:
model.cpp:613:10: warning: unused variable ‘maxVIF’ [-Wunused-variable]
  613 |   double maxVIF = 0;
      |          ^~~~~~
model.cpp: In member function ‘double Model::buildQFAM(Individual*)’:
model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type]
  849 |     error("Internal problem with QFAM model specification");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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]
   73 |        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]
   66 |   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]
  327 |   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 glm.cpp
In file included from helper.h:24,
                 from glm.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from glm.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  294 |    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]
  344 |        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]
  355 |        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]
  423 |    for (int c=0; c<conditioner.size(); c++)
      |                  ~^~~~~~~~~~~~~~~~~~~
glm.cpp:610:28: warning: ‘df’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  610 |    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 dcdflib.cpp
dcdflib.cpp: In function ‘void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:1882:36: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 1882 |     if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160;
      |                        ~~~~~~~~~~~~^~~~~~~~~~~
dcdflib.cpp: In function ‘void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:3544:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 3544 |         if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280;
      |              ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)’:
dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6025 |     if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp:6088:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6088 |     qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0;
      |           ~~~~~~^~~~~~~~~~~~~
dcdflib.cpp:6112:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6112 |     qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0;
      |            ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6153:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6153 |     qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0;
      |            ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6020:56: warning: variable ‘qok’ set but not used [-Wunused-but-set-variable]
 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup;
      |                                                        ^~~
dcdflib.cpp: In function ‘double dlanor(double*)’:
dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6401 |     if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘double dstrem(double*)’:
dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6782 |     if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)’:
dcdflib.cpp:6996:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6996 |     qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
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 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]
   73 |        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]
  493 |       for ( int k = 0 ; k < i->second.size(); k++)
      |                         ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘void Plink::permTestRareDistribution(Perm&)’:
elf.cpp:609:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |   for (int l=0; l< original.size(); l++)
      |                 ~^~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘vector_t Plink::testRareDistribution(Perm&, bool, std::map<Range, int2>&)’:
elf.cpp:654:16: warning: unused variable ‘pthresh’ [-Wunused-variable]
  654 |   const double pthresh = 0.01;
      |                ^~~~~~~
elf.cpp:655:8: warning: unused variable ‘one_sided’ [-Wunused-variable]
  655 |   bool one_sided = true;
      |        ^~~~~~~~~
elf.cpp:707:7: warning: unused variable ‘srange_cnt’ [-Wunused-variable]
  707 |   int srange_cnt = 0;
      |       ^~~~~~~~~~
elf.cpp:708:8: warning: unused variable ‘inRange’ [-Wunused-variable]
  708 |   bool inRange = false;
      |        ^~~~~~~
elf.cpp: In member function ‘void Plink::displayRareRange()’:
elf.cpp:895:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  895 |   for (int i = 0 ; i < tokens.size() ; i++)
      |                    ~~^~~~~~~~~~~~~~~
elf.cpp:939:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  939 |       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]
  374 |   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]
 1154 |        ++(*p_gcnt);
      |        ^~~~~~~~~~~
elf.cpp:1165:5: warning: ‘p_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1165 |     ++(*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 dfam.cpp
In file included from dfam.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
dfam.cpp: In member function ‘std::vector<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]
   76 |       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]
   86 |               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]
   96 |               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]
  106 |      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]
  157 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
dfam.cpp:239:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  239 |        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]
  271 |        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]
  378 |        for (int c=0; c<family[f]->kid.size(); c++)
      |                      ~^~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:218:9: warning: unused variable ‘informative’ [-Wunused-variable]
  218 |    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]
  504 |      for (int c=0; c<klist[k]->person.size(); c++)
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:151:11: warning: unused variable ‘totalInformative’ [-Wunused-variable]
  151 |       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 fisher.cpp
In file included from helper.h:24,
                 from fisher.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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:261:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  261 |       prterr(1, "NROW must be less than or equal to LDTABL.");
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:267:14: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  267 |    prterr(2, "All elements of TABLE must be positive.");
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  272 |       prterr(3, "All elements of TABLE are zero.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  273 |       "PRT and PRE are set to missing values.");
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)’:
fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  448 |     prterr(1, "NROW must be less than or equal to LDTABL.");
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  450 |     prterr(4, "NCOL must be at least 2");
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:449:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  449 |   if (*ncol <= 1)
      |   ^~
fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  453 |     for (i = 1; i <= *ldkey << 1; ++i) {
      |     ^~~
fisher.cpp:501:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  501 |        prterr(2, "All elements of TABLE must be positive.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  508 |       prterr(3, "All elements of TABLE are zero.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  509 |              "PRT and PRE are set to missing values.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  559 |       prterr(5, "The hash table key cannot be computed because "
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  560 |              "the largest key\n"
      |              ~~~~~~~~~~~~~~~~~~~
  561 |              "is larger than the largest representable int.\n"
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  562 |              "The algorithm cannot proceed.\n"
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  563 |              "Reduce the workspace size, or use `exact = FALSE'.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  750 |       prterr(6, "LDKEY is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  751 |              "Try increasing the size of the workspace.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)’:
fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1538 |       prterr(6, "LDKEY is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1539 |              "Try increasing the size of the workspace.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1554:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1554 |      prterr(7, "LDSTP is too small for this problem.\n"
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1555 |         "Try increasing the size of the workspace.");
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1596 |       prterr(7, "LDSTP is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1597 |              "Try increasing the size of the workspace.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘int iwork(int, int*, int, int)’:
fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 2001 |       prterr(40, "Out of workspace.");
      |                  ^~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void isort(int*, int*)’:
fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 2078 |       prterr(20, "This should never occur.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
linput.cpp: In member function ‘void Plink::readDataLongFormat()’:
linput.cpp:68:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |       for (int l=0; l< locus.size(); l++)
      |                     ~^~~~~~~~~~~~~~
linput.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |       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]
  136 |       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]
  146 |       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]
  164 |        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]
  200 |   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]
  209 |   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 sockets.cpp
In file included from helper.h:24,
                 from sockets.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
sockets.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > socketConnection(Plink*, std::string, int, std::string)’:
sockets.cpp:78:24: warning: unused variable ‘out_buf’ [-Wunused-variable]
   78 |   char                 out_buf[BUF_SIZE+1];  // Output buffer for GET request
      |                        ^~~~~~~
sockets.cpp:79:24: warning: unused variable ‘in_buf’ [-Wunused-variable]
   79 |   char                 in_buf[BUF_SIZE+1];   // Input buffer for response
      |                        ^~~~~~
sockets.cpp:81:24: warning: unused variable ‘i’ [-Wunused-variable]
   81 |   unsigned int         i;                    // Loop counter
      |                        ^
sockets.cpp:119:7: warning: unused variable ‘echoStringLen’ [-Wunused-variable]
  119 |   int echoStringLen = 100;
      |       ^~~~~~~~~~~~~
g++ -Wall -g  -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
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]
   73 |        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]
  206 |      for (int i=25; i<tokens.size()-1; i++)
      |                     ~^~~~~~~~~~~~~~~~
lookup.cpp:203:8: warning: unused variable ‘totalSNPs’ [-Wunused-variable]
  203 |    int totalSNPs = 0;
      |        ^~~~~~~~~
lookup.cpp:204:8: warning: unused variable ‘gcount’ [-Wunused-variable]
  204 |    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]
  272 |        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]
  289 |    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 proxy.cpp
In file included from proxy.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from proxy.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  314 |       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]
  332 |    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]
  854 |    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]
 1332 |    for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1401 |       for (int c1 = 0; c1 < collection.size() ; c1++ )
      |                        ~~~^~~~~~~~~~~~~~~~~~~
proxy.cpp:1448:12: warning: unused variable ‘t1’ [-Wunused-variable]
 1448 |        int t1=0;
      |            ^~
proxy.cpp:169:10: warning: unused variable ‘s’ [-Wunused-variable]
  169 |   CSNP * s = SNP[l];
      |          ^
proxy.cpp:939:58: warning: ‘ref’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  939 |      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 pdriver.cpp
In file included from pdriver.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from pdriver.cpp:18:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  266 |       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 haploQTL.cpp
In file included from haploQTL.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from haploQTL.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
   83 |    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]
  145 |    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 haplohelper.cpp
In file included from haplohelper.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from haplohelper.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
   27 |     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]
   34 |     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]
  104 |       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]
  134 |   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]
  297 |   for (int h=0; h<hap.size(); h++)
      |                 ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::setTestHaplotype(std::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]
  337 |   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]
  396 |    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]
  413 |     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]
  487 |    for (int z = 0; z < hap1[i].size(); z++)
      |                    ~~^~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘vector_t HaploPhase::imputeGenotype(int, int)’:
haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  655 |   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]
  754 |       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]
  802 |    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]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |       ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |                            ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |                                                 ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  851 |       ||alleles2.size() != ns )
      |         ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘double HaploPhase::freq(boolvec_t&, boolvec_t&)’:
haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  957 |   if (mask1.size() != ns ||alleles1.size() != ns )
      |       ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  957 |   if (mask1.size() != ns ||alleles1.size() != ns )
      |                            ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘void HaploPhase::trackThisSegment()’:
haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1225 |       for (int z = 0; z < hap1[p1].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1251 |       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]
 1252 |  for (int z2 = 0; z2 < hap1[p2].size(); z2++)
      |                   ~~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1250:11: warning: unused variable ‘j’ [-Wunused-variable]
 1250 |       int j=0;
      |           ^
haplohelper.cpp: In member function ‘void HaploPhase::calculateEmpiricalVariance(std::set<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]
 1419 |   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]
 1477 |     for( int z = 0; z < pp[i].size(); z++ )
      |                     ~~^~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::verboseDisplayWindows(int, bool)’:
haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1666 |       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 haplowindow.cpp
In file included from haplowindow.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from haplowindow.cpp:27:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
   27 |     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]
   34 |     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]
   48 |       for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::enumerateHaplotypes(intvec_t&)’:
haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  183 |   while (h<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]
  558 |   for (int z=0; z < hap1[i].size(); z++)
      |                 ~~^~~~~~~~~~~~~~~~
haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  574 |       for (int z=0; z < new_pp.size(); z++)
      |                     ~~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::performEM()’:
haplowindow.cpp:683:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  683 |     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]
  691 |     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]
  751 |        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]
  791 |     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]
  798 |     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]
  868 |     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]
  872 |   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]
  949 |    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]
  966 |     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 genogroup.cpp
In file included from genogroup.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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]
  252 |       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]
   27 |     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]
   34 |     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 nonfounderphasing.cpp
In file included from nonfounderphasing.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from nonfounderphasing.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
  668 |     for (int z=0; z < pp[i].size(); z++)
      |                   ~~^~~~~~~~~~~~~~
nonfounderphasing.cpp:360:7: warning: unused variable ‘pcnt’ [-Wunused-variable]
  360 |   int pcnt=1;
      |       ^~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::transmissionCount(int, std::map<FamilyTransmissions, double>&)’:
nonfounderphasing.cpp:715:14: warning: unused variable ‘posterior’ [-Wunused-variable]
  715 |       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 clumpld.cpp
In file included from helper.h:24,
                 from clumpld.h:21,
                 from clumpld.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from clumpld.cpp:21:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
clumpld.cpp: In member function ‘std::vector<ResultTrio> clump_LD::read_assoc_file(std::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]
   92 |   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]
  128 |       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]
  137 |      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]
  173 |    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]
  174 |         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]
  201 |        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]
  204 |     if ( f < annot_field.size() - 1 )
      |          ~~^~~~~~~~~~~~~~~~~~~~~~~~
clumpld.cpp: In member function ‘void clump_LD::clump()’:
clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResultTrio>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  368 |   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]
  480 |    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]
  520 |     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]
  611 |     for (int f=1; f<=filename.size(); f++)
      |                   ~^~~~~~~~~~~~~~~~~
clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int2, double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1097 |               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 genoerr.cpp
In file included from genoerr.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from genoerr.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
  157 |   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]
  189 |       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]
  190 |  for( int b = 0; b < posshap2.size(); b++ )
      |                  ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  225 |   for (int z = 0; z < new_hap1.size(); z++)
      |                   ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |       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]
  328 |        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]
  347 |       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]
  358 |    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 em.cpp
In file included from em.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from em.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
   89 |         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]
   97 |         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]
  106 |     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]
  128 |     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]
  132 |   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]
  162 |         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]
  166 |       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 impute.cpp
In file included from impute.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from impute.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
   40 |     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]
  105 |    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]
  144 |        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]
  161 |        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]
  263 |    for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++)
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp:313:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<probabilisticGenotype>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  313 |       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 metaem.cpp
In file included from metaem.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from metaem.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     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]
   34 |     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]
  252 |       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]
  239 |    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 profile.cpp
In file included from profile.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::scoreIndividuals()’:
profile.cpp:303:12: warning: unused variable ‘OLD_assoc_glm_without_main_snp’ [-Wunused-variable]
  303 |       bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp;
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profile.cpp:304:12: warning: unused variable ‘OLD_clist’ [-Wunused-variable]
  304 |       bool OLD_clist = par::clist;
      |            ^~~~~~~~~
profile.cpp:350:14: warning: unused variable ‘statistic’ [-Wunused-variable]
  350 |       double statistic = valid ? model->getStatistic() : 0;
      |              ^~~~~~~~~
profile.cpp:351:14: warning: unused variable ‘pvalue’ [-Wunused-variable]
  351 |       double pvalue = pval[ pval.size()-1 ];
      |              ^~~~~~
profile.cpp:352:14: warning: unused variable ‘beta’ [-Wunused-variable]
  352 |       double beta = b[ b.size()-1 ];
      |              ^~~~
profile.cpp:390:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  390 |       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]
  402 |    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]
  421 |   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]
  480 |    bool a1 = i2->second;
      |         ^~
profile.cpp:525:9: warning: variable ‘sawNamedAllele’ set but not used [-Wunused-but-set-variable]
  525 |    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]
  629 |    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]
  667 |   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 nlist.cpp
In file included from helper.h:24,
                 from nlist.h:21,
                 from nlist.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseNumberList(std::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]
   38 |   for (int i=0; i<tok.size(); i++)
      |                 ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseStringList(std::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]
   83 |   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]
  107 |   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]
  124 |   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]
  151 |   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]
  160 |       for (int i=0; i<n.size(); i++)
      |                     ~^~~~~~~~~
nlist.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > NList::tokenize(std::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]
  189 |   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]
  239 |    if ( s[i]== range_char && i == s.length()-1 )
      |                              ~~^~~~~~~~~~~~~~~
nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  253 |       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 whap.cpp
In file included from helper.h:24,
                 from whap.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from whap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  334 |       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]
  393 |        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]
  454 |       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]
  456 |       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]
  508 |   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]
  511 |       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]
  619 |       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]
  670 |       for (int s=0; s < conditioner.size(); s++)
      |                     ~~^~~~~~~~~~~~~~~~~~~~
whap.cpp:793:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  793 |    if ( p1 != coeff1.size() || p0 != coeff0.size() )
      |         ~~~^~~~~~~~~~~~~~~~
whap.cpp:793:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  793 |    if ( p1 != coeff1.size() || p0 != coeff0.size() )
      |                                ~~~^~~~~~~~~~~~~~~~
whap.cpp: In member function ‘void Chap::build(ChapModel&)’:
whap.cpp:962:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  962 |       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]
  986 |       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]
 1015 |        for (int i=0; i< tok.size(); i++)
      |                      ~^~~~~~~~~~~~
whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1048 |       for ( int i = 0 ; i < tok.size() ; i++ )
      |                         ~~^~~~~~~~~~~~
whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1118 |       if ( mapping.size() != H->ns + H->nh )
      |            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1129 |       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]
 1142 |    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]
 1162 |        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]
 1197 |       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]
 1231 |    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]
 1290 |   for (int g=0; g< model.group.size(); g++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1326 |       for (int c=0; c < P->conditioner.size(); c++)
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1334 |       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]
 1389 |   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]
 1425 |   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]
 1434 |    if ( cnt>0 && cnt2 < m.group[h].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 simul.cpp
In file included from helper.h:24,
                 from simul.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
simul.cpp: In function ‘vector_t instanceSNP(SimParameters&)’:
simul.cpp:172:10: warning: unused variable ‘gh_11_12’ [-Wunused-variable]
  172 |   double gh_11_12 = h11*h12;
      |          ^~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs()’:
simul.cpp:635:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  635 |   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]
  679 |   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]
 1146 |   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]
 1211 |   for (int s=0; s<sp.size(); s++)
      |                 ~^~~~~~~~~~
simul.cpp:1358:23: warning: unused variable ‘cumU’ [-Wunused-variable]
 1358 |      double cumA = 0, cumU = 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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
gvar.cpp: In member function ‘void Plink::readGenericVariantData()’:
gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  125 |       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]
  192 |       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]
  247 |   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]
  298 |    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]
  381 |       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]
  395 |       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]
  403 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
gvar.cpp:471:11: warning: unused variable ‘ip’ [-Wunused-variable]
  471 |       int ip = peri->second;
      |           ^~
gvar.cpp:414:8: warning: unused variable ‘fatal’ [-Wunused-variable]
  414 |   bool fatal = false;
      |        ^~~~~
gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  549 |       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]
  553 |  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]
  556 |  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 cnv.cpp
In file included from helper.h:24,
                 from cnv.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘void Plink::readCNVList()’:
cnv.cpp:247:8: warning: unused variable ‘p1’ [-Wunused-variable]
  247 |    int p1,p2;
      |        ^~
cnv.cpp:247:11: warning: unused variable ‘p2’ [-Wunused-variable]
  247 |    int p1,p2;
      |           ^~
cnv.cpp:332:12: warning: unused variable ‘p1’ [-Wunused-variable]
  332 |        int p1,p2;
      |            ^~
cnv.cpp:332:15: warning: unused variable ‘p2’ [-Wunused-variable]
  332 |        int p1,p2;
      |               ^~
cnv.cpp:678:36: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
  678 |        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]
  815 |       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]
  825 |    for (int s2=s1+1; s2<segment.size(); s2++)
      |                      ~~^~~~~~~~~~~~~~~
cnv.cpp:916:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  916 |  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’
  922 |    isection.clear();
      |    ^~~~~~~~
cnv.cpp:1031:25: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable]
 1031 |    set<Range>::iterator i2 = isection.begin();
      |                         ^~
cnv.cpp:1103:36: warning: variable ‘il’ set but not used [-Wunused-but-set-variable]
 1103 |    map<indivPair,double>::iterator il = segmentLength.find(t);
      |                                    ^~
cnv.cpp:1414:11: warning: unused variable ‘nseg’ [-Wunused-variable]
 1414 |       int nseg = 1;
      |           ^~~~
cnv.cpp:412:7: warning: unused variable ‘nseg’ [-Wunused-variable]
  412 |   int nseg=0;
      |       ^~~~
cnv.cpp: In function ‘double weighted_count_intersects(std::set<Range>&, int, int, int)’:
cnv.cpp:1749:7: warning: unused variable ‘cnt’ [-Wunused-variable]
 1749 |   int cnt = 0;
      |       ^~~
cnv.cpp: In member function ‘void Plink::positionPermuteSegments()’:
cnv.cpp:2013:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, CInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2013 |   for (int c = 0 ; c < scaffold.size(); c++)
      |                    ~~^~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘vector_t Plink::glmCNVBurdenModel(Perm&, bool)’:
cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value]
 2098 |     noCovar == true;
      |     ~~~~~~~~^~~~~~~
cnv.cpp:2202:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
 2202 |       indivPair p = ic->first;
      |                 ^
cnv.cpp:2288:10: warning: unused variable ‘statistic’ [-Wunused-variable]
 2288 |   double statistic = valid ? model->getStatistic() : 0;
      |          ^~~~~~~~~
cnv.cpp:2289:10: warning: unused variable ‘pvalue’ [-Wunused-variable]
 2289 |   double pvalue = pval[ pval.size()-1 ];
      |          ^~~~~~
cnv.cpp:2290:10: warning: unused variable ‘beta’ [-Wunused-variable]
 2290 |   double beta = b[ b.size()-1 ];
      |          ^~~~
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]
 1500 |       CInfo cdet;
      |             ^~~~
cnv.cpp:1500:13: warning: ‘cdet.CInfo::lstop’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -Wall -g  -fdebug-prefix-map=/<<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 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]
   73 |        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 greport.cpp
In file included from greport.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
greport.cpp: In member function ‘void Plink::displayGeneReport()’:
greport.cpp:78:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |   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]
  147 |       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]
  148 |     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]
  156 |    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]
  169 |    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]
  240 |        for (int l=0; l< ari->second.size(); l+=2)
      |                      ~^~~~~~~~~~~~~~~~~~~~
greport.cpp:125:7: warning: unused variable ‘cnt’ [-Wunused-variable]
  125 |   int cnt = 0;
      |       ^~~
g++ -Wall -g  -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 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]
   73 |        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 qualscores.cpp
In file included from helper.h:24,
                 from qualscores.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
qualscores.cpp: In member function ‘void Plink::filterQualGenotypes()’:
qualscores.cpp:122:12: warning: unused variable ‘nfound’ [-Wunused-variable]
  122 |   long int nfound = 0;
      |            ^~~~~~
g++ -Wall -g  -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 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]
   73 |        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 cfamily.cpp
In file included from cfamily.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
cfamily.cpp: In function ‘int mCount(Individual*, Individual*)’:
cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  205 |       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]
  221 |        for (int j = 0 ; j < inds[i]->kids.size() ; j++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |        for (int i = 0 ; i < inds.size() ; i++)
      |                         ~~^~~~~~~~~~~~~
cfamily.cpp: In function ‘bool isAncestorOf(Individual*, Individual*)’:
cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  263 |       for (int i = 0 ; i < inds.size() ; i++)
      |                        ~~^~~~~~~~~~~~~
cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  276 |               for (int j = 0 ; j < inds[i]->kids.size() ; j++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  288 |       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 setscreen.cpp
In file included from setscreen.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
setscreen.cpp: In member function ‘void Plink::setAssocSummary()’:
setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   80 |   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]
  110 |       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]
  188 |   for ( int j = 0; j < pS->snpset.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  196 |       for (int i=0; i < snpset[j].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 idhelp.cpp
In file included from idhelp.cpp:18:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  196 |     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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘std::map<IDField*, std::set<IDValue> > IDHelper::parseQuery(std::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]
   40 |   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]
   63 |    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]
  136 |   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]
  169 |   if ( found != matchTemplate.size() )
      |        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:128:8: warning: unused variable ‘match’ [-Wunused-variable]
  128 |   bool match = true;
      |        ^~~~~
idhelp.cpp: In member function ‘void IDHelper::setJointValues(IDGroup*)’:
idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int j = 0 ; j < jointField.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |       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]
  296 |    for ( int i = 0 ; i < mask.size() ; i++)
      |                      ~~^~~~~~~~~~~~~
idhelp.cpp:214:26: warning: unused variable ‘jo’ [-Wunused-variable]
  214 |       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]
  346 |   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]
  502 |    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]
  510 |       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]
  542 |     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]
  547 |     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]
  553 |     for (int i = 0 ; i < ids.size() ; i++)
      |                      ~~^~~~~~~~~~~~
idhelp.cpp:529:10: warning: unused variable ‘seenJoint’ [-Wunused-variable]
  529 |     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]
  584 |     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]
  594 |     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]
  678 |        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]
  727 |   for ( int f = 0 ; f < files.size() ; f++ )
      |                     ~~^~~~~~~~~~~~~~
idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  742 |   for (int j = 0 ; j < jointField.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  745 |       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]
  747 |    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]
  757 |         for ( int j = 0; j < files[f].fields.size(); j++)
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:744:23: warning: unused variable ‘jf’ [-Wunused-variable]
  744 |       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]
  772 |       for (int j = 0 ; j < jointField.size(); j++ )
      |                        ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  790 |   for ( int f = 0 ; f < files.size() ; f++ )
      |                     ~~^~~~~~~~~~~~~~
idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  794 |       for ( int j = 0 ; j < files[f].fields.size(); j++ )
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  808 |       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]
  836 |     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]
  888 |    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]
  894 |        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]
  903 |     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]
  922 |    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]
  950 |     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]
  975 |     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]
 1000 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1003 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1013 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1015:17: warning: unused variable ‘group’ [-Wunused-variable]
 1015 |       IDGroup * group = idgroup[g];
      |                 ^~~~~
idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1025 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1028 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1031:14: warning: unused variable ‘v’ [-Wunused-variable]
 1031 |    IDValue & v = *(group->values[j]);
      |              ^
idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1070 |       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]
 1085 |    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]
 1110 |    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]
 1128 |        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]
 1183 |          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]
 1189 |          for (int z=0; z<(*i0)->values.size(); z++)
      |                        ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1236 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1242 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1245:14: warning: unused variable ‘v’ [-Wunused-variable]
 1245 |    IDValue & v = *(group->values[j]);
      |              ^
idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1346 |       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]
 1424 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1440 |       for ( int j = 0; j < group->values.size(); j++ )
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idReplace()’:
idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1551 |   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]
 1631 |       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]
 1648 |       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]
 1649 |  for (int i = 0 ; i < tokens.size(); i++)
      |                   ~~^~~~~~~~~~~~~~~
idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1654 |       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]
 1675 |   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]
 1684 |       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]
 1692 |    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]
 1710 |    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]
 1733 |        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]
 1735 |     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]
 1770 |        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]
 1784 |        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]
 1801 |       for (int i = 0 ; i < tokens.size() ; i++ )
      |                        ~~^~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idMatch()’:
idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1856 |   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]
 1903 |    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]
 1937 |    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]
 1957 |    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]
 1964 |        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]
 1986 |    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]
 2018 |      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]
 2024 |   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]
 2030 |    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]
 2034 |    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]
 2070 |     for (int v=0; v<g->values.size(); v++)
      |                   ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1889:12: warning: unused variable ‘jointQuery’ [-Wunused-variable]
 1889 |       bool jointQuery = id.find("+") != string::npos;
      |            ^~~~~~~~~~
idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2167 |       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]
 2168 |  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]
 2201 |        for (int k = 0 ; k < thisLine.size() ; k++ )
      |                         ~~^~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idDump()’:
idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2229 |   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]
 2234 |    for (int j = 0 ; j < group->values.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 tag.cpp
In file included from helper.h:24,
                 from tag.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        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 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]
   73 |        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]
  252 |       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 lookup2.cpp
In file included from helper.h:24,
                 from lookup2.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
lookup2.cpp: In member function ‘void Plink::lookup2()’:
lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  203 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  280 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  325 |    for (int t = 0 ; t < tokens.size() ; t++)
      |                     ~~^~~~~~~~~~~~~~~
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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from blox.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  147 |       int nsnps = toPosition - fromPosition + 1;
      |           ^~~~~
blox.cpp:156:11: warning: unused variable ‘numStrong’ [-Wunused-variable]
  156 |       int numStrong = 0;
      |           ^~~~~~~~~
blox.cpp:157:11: warning: unused variable ‘numRec’ [-Wunused-variable]
  157 |       int numRec = 0;
      |           ^~~~~~
blox.cpp:158:11: warning: unused variable ‘numInGroup’ [-Wunused-variable]
  158 |       int numInGroup = 0;
      |           ^~~~~~~~~~
blox.cpp:226:11: warning: unused variable ‘cnt’ [-Wunused-variable]
  226 |       int cnt = 0;
      |           ^~~
blox.cpp:418:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  418 |       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]
  427 |       for (int k=0; k<b.size(); k++)
      |                     ~^~~~~~~~~
blox.cpp:123:16: warning: unused variable ‘fourGameteCutoff’ [-Wunused-variable]
  123 |   const double fourGameteCutoff = 0.01;
      |                ^~~~~~~~~~~~~~~~
blox.cpp: In member function ‘void PairwiseLinkage::calculateCI()’:
blox.cpp:469:7: warning: unused variable ‘total_chroms’ [-Wunused-variable]
  469 |   int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH;
      |       ^~~~~~~~~~~~
blox.cpp:569:41: warning: ‘pB2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  569 |   if ( pB1>0 ) loglike1 += knownBA * log( pB1 );
      |                                      ~~~^~~~~~~
blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  505 |   double p1 = pA1 + pB1;
      |          ^~
blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  503 |   double pA = pA1 + pA2;
      |          ^~
blox.cpp:510:10: warning: ‘pA1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  510 |   double D = pA1 - (pA*p1);
      |          ^
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 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]
   73 |        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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from dosage.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       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]
  110 |        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]
  513 |    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]
  548 |       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]
  581 |    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]
  601 |    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]
  695 |    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]
  750 |        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]
  989 |     for (int q=0; q<inQ.size(); q++)
      |                   ~^~~~~~~~~~~
dosage.cpp:1170:11: warning: unused variable ‘statistic’ [-Wunused-variable]
 1170 |    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]
 1252 |    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]
 1310 |    if ( ++qq == qthresh.size() )
      |         ~~~~~^~~~~~~~~~~~~~~~~
dosage.cpp:190:7: warning: unused variable ‘geno_field’ [-Wunused-variable]
  190 |   int geno_field = a2_field + skip2 + 1;
      |       ^~~~~~~~~~
dosage.cpp:915:21: warning: ‘snp_code’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  915 |         SNP[snp_code]->one[personPosition[f][i]] = s1;
      |                     ^
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 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]
   73 |        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]
   83 |    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]
  149 |   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]
  250 |    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]
  251 |         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]
  260 |    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]
  275 |    if ( tokens.size() <= snp_column )
      |         ~~~~~~~~~~~~~~^~~~~~~~~~~~~
annot.cpp:300:9: warning: unused variable ‘include’ [-Wunused-variable]
  300 |    bool include = 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 metaanal.cpp
In file included from metaanal.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
metaanal.cpp: In constructor ‘Alleles::Alleles(std::string, int, int, std::string, std::string)’:
metaanal.cpp:47:7: warning: ‘Alleles::bp’ will be initialized after [-Wreorder]
   47 |   int bp;
      |       ^~
metaanal.cpp:44:10: warning:   ‘std::string Alleles::a1’ [-Wreorder]
   44 |   string a1;
      |          ^~
metaanal.cpp:61:3: warning:   when initialized here [-Wreorder]
   61 |   Alleles(string name, int chr, int bp, string a1, string a2)
      |   ^~~~~~~
metaanal.cpp: In member function ‘void Plink::metaAnalysis()’:
metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  159 |       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]
  182 |       for (int f=0; f<ns.size(); f++)
      |                     ~^~~~~~~~~~
metaanal.cpp:203:18: warning: statement has no effect [-Wunused-value]
  203 |     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]
  213 |    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]
  235 |   for (int f = 0 ; f < par::meta_files.size() ; f++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  261 |       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]
  300 |    if ( tokens.size() != fsize )
      |         ~~~~~~~~~~~~~~^~~~~~~~
metaanal.cpp:253:11: warning: variable ‘pval_column’ set but not used [-Wunused-but-set-variable]
  253 |       int pval_column = -1;
      |           ^~~~~~~~~~~
metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  482 |     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]
  637 |      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]
  680 |      for (int f=0; f<par::meta_files.size(); f++)
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
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 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]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
In file included from r.cpp:29:
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’:
Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  203 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’:
Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  206 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’:
Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  232 |     char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; }
      |                                          ~^~~~~
Rconnection.h: In member function ‘void Rstrings::decode()’:
Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare]
  245 |       while (i < len) { if (!c[i]) nel++; i++; }
      |              ~~^~~~~
Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |  while (i < nel) {
      |         ~~^~~~~
r.cpp: In member function ‘void Plink::Rfunc()’:
r.cpp:330:8: warning: unused variable ‘ct’ [-Wunused-variable]
  330 |    int ct = data->length();
      |        ^~
r.cpp:380:9: warning: ‘rCov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  380 |  delete rCov;
      |         ^~~~
r.cpp:378:14: warning: ‘rS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  378 |       delete rS;
      |              ^~
r.cpp:377:14: warning: ‘rP’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  377 |       delete rP;
      |              ^~
r.cpp:376:14: warning: ‘rN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  376 |       delete rN;
      |              ^~
r.cpp:399:10: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  399 |   delete rc;
      |          ^~
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 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]
  203 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’:
Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  206 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’:
Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  232 |     char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; }
      |                                          ~^~~~~
Rconnection.h: In member function ‘void Rstrings::decode()’:
Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare]
  245 |       while (i < len) { if (!c[i]) nel++; i++; }
      |              ~~^~~~~
Rconnection.h:249:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |  while (i < nel) {
      |         ~~^~~~~
Rconnection.cpp: At global scope:
Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */
      |                    ^~~~~~~~~~~~~~
Rconnection.cpp: In destructor ‘virtual Rconnection::~Rconnection()’:
Rconnection.cpp:567:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  567 |     if (host) free(host); host=0;
      |     ^~
Rconnection.cpp:567:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  567 |     if (host) free(host); host=0;
      |                           ^~~~
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
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 2019-10-14T10:21:11Z

Finished
--------


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

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

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 355904
Build-Time: 408
Distribution: unstable
Fail-Stage: build
Foreign Architectures: armel
Host Architecture: armel
Install-Time: 16
Job: plink_1.07+dfsg-2
Machine Architecture: amd64
Package: plink
Package-Time: 436
Source-Version: 1.07+dfsg-2
Space: 355904
Status: attempted
Version: 1.07+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-10-14T10:21:11Z
Build needed 00:07:16, 355904k disk space