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

+==============================================================================+
| plink 1.07+dfsg-3 (mipsel)                   Mon, 06 Apr 2020 12:00:12 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-3
Source Version: 1.07+dfsg-3
Distribution: unstable
Machine Architecture: amd64
Host Architecture: mipsel
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-0c769f71-a7fc-4923-b08b-b34699544188' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-0c4eBt/resolver-bJSVI6' with '<<RESOLVERDIR>>'

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

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 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 2020-04-06-0801.17.pdiff [5225 B]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-04-06-0801.17.pdiff [5225 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-04-06-0801.17.pdiff [4499 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-04-06-0801.17.pdiff [4499 B]
Get:6 http://debian.oregonstate.edu/debian unstable/main mipsel Packages [7912 kB]
Fetched 8124 kB in 1s (5545 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-3 (dsc) [2079 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-3 (tar) [429 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-3 (diff) [16.8 kB]
Fetched 448 kB in 0s (8408 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-0c4eBt/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-0c4eBt' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64, libc-dev:mipsel, libstdc++-dev:mipsel
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64, libc-dev:mipsel, libstdc++-dev:mipsel
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 [410 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [498 B]
Fetched 1865 B in 0s (73.2 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-mipsel-linux-gnu
  bsdmainutils build-essential cpp-9-mipsel-linux-gnu cpp-mipsel-linux-gnu
  cross-config crossbuild-essential-mipsel debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-mipsel-linux-gnu
  g++-mipsel-linux-gnu gcc-10-base:mipsel gcc-10-cross-base-mipsen
  gcc-8-base:mipsel gcc-9-cross-base-mipsen gcc-9-mipsel-linux-gnu
  gcc-9-mipsel-linux-gnu-base gcc-mipsel-linux-gnu gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libatomic1:mipsel
  libatomic1-mipsel-cross libbsd0 libc6:mipsel libc6-dev libc6-dev:mipsel
  libc6-dev-mipsel-cross libc6-mipsel-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:mipsel
  libcrypt1:mipsel libdebhelper-perl libdebian-dpkgcross-perl libelf1
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-8-dev:mipsel libgcc-9-dev-mipsel-cross libgcc-s1:mipsel
  libgcc-s1-mipsel-cross libglib2.0-0 libgomp1:mipsel libgomp1-mipsel-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libpipeline1 libsigsegv2 libstdc++-8-dev:mipsel libstdc++-9-dev
  libstdc++-9-dev-mipsel-cross libstdc++6:mipsel libstdc++6-mipsel-cross
  libsub-override-perl libtool libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mipsel
  linux-libc-dev-mipsel-cross m4 man-db po-debconf sensible-utils ucf
  zlib1g:mipsel zlib1g-dev:mipsel
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
  | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch
  g++-multilib g++-9-multilib gcc-9-doc g++-9-multilib-mipsel-linux-gnu
  gcc-9-multilib-mipsel-linux-gnu manpages-dev flex bison gdb-mipsel-linux-gnu
  gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:mipsel
  libc-l10n:mipsel locales:mipsel glibc-doc manpages-dev:mipsel
  libstdc++-8-doc:mipsel libstdc++-9-doc 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:mipsel libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs 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-mipsel-linux-gnu
  bsdmainutils build-essential cpp-9-mipsel-linux-gnu cpp-mipsel-linux-gnu
  cross-config crossbuild-essential-mipsel debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-mipsel-linux-gnu
  g++-mipsel-linux-gnu gcc-10-base:mipsel gcc-10-cross-base-mipsen
  gcc-8-base:mipsel gcc-9-cross-base-mipsen gcc-9-mipsel-linux-gnu
  gcc-9-mipsel-linux-gnu-base gcc-mipsel-linux-gnu gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libatomic1:mipsel
  libatomic1-mipsel-cross libbsd0 libc6:mipsel libc6-dev libc6-dev:mipsel
  libc6-dev-mipsel-cross libc6-mipsel-cross libconfig-auto-perl
  libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:mipsel
  libcrypt1:mipsel libdebhelper-perl libdebian-dpkgcross-perl libelf1
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-8-dev:mipsel libgcc-9-dev-mipsel-cross libgcc-s1:mipsel
  libgcc-s1-mipsel-cross libglib2.0-0 libgomp1:mipsel libgomp1-mipsel-cross
  libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1
  libpipeline1 libsigsegv2 libstdc++-8-dev:mipsel libstdc++-9-dev
  libstdc++-9-dev-mipsel-cross libstdc++6:mipsel libstdc++6-mipsel-cross
  libsub-override-perl libtool libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mipsel
  linux-libc-dev-mipsel-cross m4 man-db po-debconf
  sbuild-build-depends-main-dummy:mipsel sensible-utils ucf zlib1g:mipsel
  zlib1g-dev:mipsel
0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded.
Need to get 74.8 MB of archives.
After this operation, 300 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 1.22.4-4 [919 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main mipsel gcc-10-base mipsel 10-20200402-1 [196 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [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 1.4.18-4 [203 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [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 0.19.8.1-10 [435 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mipsel-linux-gnu amd64 2.34-5cross6 [2309 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-4 [2629 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-10 [1699 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-10 [10.7 MB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-mipsel-linux-gnu-base amd64 9.3.0-8cross1 [196 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-mipsel-linux-gnu amd64 9.3.0-8cross1 [6465 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mipsel-linux-gnu amd64 4:9.2.1-4.1 [16.7 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base-mipsen all 9.3.0-8cross1 [192 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base-mipsen all 10-20200324-1cross1 [192 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mipsel-cross all 2.30-2cross1 [1199 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-mipsel-cross all 10-20200324-1cross1 [46.6 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mipsel-cross all 10-20200324-1cross1 [90.3 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mipsel-cross all 10-20200324-1cross1 [6652 B]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-mipsel-cross all 9.3.0-8cross1 [223 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-mipsel-linux-gnu amd64 9.3.0-8cross1 [6819 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mipsel-linux-gnu amd64 4:9.2.1-4.1 [1460 B]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mipsel-cross all 10-20200324-1cross1 [395 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mipsel-cross all 5.4.19-1cross1 [1166 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mipsel-cross all 2.30-2cross1 [2274 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-mipsel-cross all 9.3.0-8cross1 [1708 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-mipsel-linux-gnu amd64 9.3.0-8cross1 [7051 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mipsel-linux-gnu amd64 4:9.2.1-4.1 [1176 B]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-3 [8296 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-4 [709 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mipsel all 12.8 [6684 B]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.10 [184 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.1-1 [1341 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.10 [1003 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main mipsel gcc-8-base mipsel 8.4.0-3 [194 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc-s1 mipsel 10-20200402-1 [46.2 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main mipsel libcrypt1 mipsel 1:4.4.16-1 [113 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main mipsel libc6 mipsel 2.30-4 [2419 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main mipsel libatomic1 mipsel 10-20200402-1 [6708 B]
Get:84 http://debian.oregonstate.edu/debian unstable/main mipsel linux-libc-dev mipsel 5.5.13-2 [1079 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main mipsel libcrypt-dev mipsel 1:4.4.16-1 [134 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main mipsel libc6-dev mipsel 2.30-4 [2271 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main mipsel libgomp1 mipsel 10-20200402-1 [92.2 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc-8-dev mipsel 8.4.0-3 [210 kB]
Get:89 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++6 mipsel 10-20200402-1 [435 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++-8-dev mipsel 8.4.0-3 [1561 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g mipsel 1:1.2.11.dfsg-2 [88.2 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g-dev mipsel 1:1.2.11.dfsg-2 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 74.8 MB in 1s (99.2 MB/s)
Selecting previously unselected package libbsd0:amd64.
(Reading database ... 12626 files and directories currently installed.)
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Unpacking libbsd0:amd64 (0.10.0-1) ...
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Preparing to unpack .../08-sensible-utils_0.0.12+nmu1_all.deb ...
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No schema files found: doing nothing.
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Setting up libyaml-perl (1.30-1) ...
Setting up libicu63:amd64 (63.2-3) ...
Setting up libxml-sax-base-perl (1.09-1) ...
Setting up libio-string-perl (1.08-3) ...
Setting up gcc-10-base:mipsel (10-20200402-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up cross-config (2.6.15-3) ...
Setting up gcc-10-cross-base-mipsen (10-20200324-1cross1) ...
Setting up binutils-mipsel-linux-gnu (2.34-5cross6) ...
Setting up libsigsegv2:amd64 (2.12-2) ...
Setting up gcc-8-base:mipsel (8.4.0-3) ...
Setting up libgomp1-mipsel-cross (10-20200324-1cross1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up cpp-9-mipsel-linux-gnu (9.3.0-8cross1) ...
Setting up linux-libc-dev-mipsel-cross (5.4.19-1cross1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libcrypt-dev:amd64 (1:4.4.16-1) ...
Setting up libuchardet0:amd64 (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libc6-dev:amd64 (2.30-4) ...
Setting up libfile-homedir-perl (1.004-1) ...
Setting up libbsd0:amd64 (0.10.0-1) ...
Setting up libelf1:amd64 (0.176-1.1) ...
Setting up libxml2:amd64 (2.9.10+dfsg-4) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libstdc++-9-dev:amd64 (9.3.0-10) ...
Setting up libc6-dev-mipsel-cross (2.30-2cross1) ...
Setting up libtool (2.4.6-14) ...
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Setting up m4 (1.4.18-4) ...
Setting up libatomic1-mipsel-cross (10-20200324-1cross1) ...
Setting up libgcc-9-dev-mipsel-cross (9.3.0-8cross1) ...
Setting up cpp-mipsel-linux-gnu (4:9.2.1-4.1) ...
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 g++-9 (9.3.0-10) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up g++ (4:9.2.1-3.1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up build-essential (12.8) ...
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 gcc-9-mipsel-linux-gnu (9.3.0-8cross1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++6-mipsel-cross (10-20200324-1cross1) ...
Setting up man-db (2.9.1-1) ...
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 gcc-mipsel-linux-gnu (4:9.2.1-4.1) ...
Setting up libxml-libxml-perl (2.0134+dfsg-2) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libstdc++-9-dev-mipsel-cross (9.3.0-8cross1) ...
Setting up po-debconf (1.0.21) ...
Setting up g++-9-mipsel-linux-gnu (9.3.0-8cross1) ...
Setting up g++-mipsel-linux-gnu (4:9.2.1-4.1) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up libconfig-auto-perl (0.44-1) ...
Setting up libdebian-dpkgcross-perl (2.6.15-3) ...
Setting up dpkg-cross (2.6.15-3) ...
Setting up crossbuild-essential-mipsel (12.8) ...
Setting up libcrypt1:mipsel (1:4.4.16-1) ...
Setting up libgcc-s1:mipsel (10-20200402-1) ...
Setting up libc6:mipsel (2.30-4) ...
Setting up libcrypt-dev:mipsel (1:4.4.16-1) ...
Setting up libc6-dev:mipsel (2.30-4) ...
Setting up libstdc++6:mipsel (10-20200402-1) ...
Setting up zlib1g:mipsel (1:1.2.11.dfsg-2) ...
Setting up libgomp1:mipsel (10-20200402-1) ...
Setting up dh-autoreconf (19) ...
Setting up libatomic1:mipsel (10-20200402-1) ...
Setting up libgcc-8-dev:mipsel (8.4.0-3) ...
Setting up zlib1g-dev:mipsel (1:1.2.11.dfsg-2) ...
Setting up libstdc++-8-dev:mipsel (8.4.0-3) ...
Setting up debhelper (12.10) ...
Setting up sbuild-build-depends-main-dummy:mipsel (0.invalid.0) ...
Processing triggers for libc-bin (2.30-4) ...

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

Arch check ok (mipsel included in any)

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

Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64)
Toolchain package versions: binutils_2.34-5 dpkg-dev_1.19.7 g++-9_9.3.0-10 gcc-9_9.3.0-10 libc6-dev_2.30-4 libstdc++-8-dev_8.4.0-3 libstdc++-9-dev_9.3.0-10 libstdc++-9-dev-mipsel-cross_9.3.0-8cross1 libstdc++6_10-20200402-1 libstdc++6-mipsel-cross_10-20200324-1cross1 linux-libc-dev_5.5.13-2
Package versions: adduser_3.118 apt_2.0.1 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5 binutils-common_2.34-5 binutils-mipsel-linux-gnu_2.34-5cross6 binutils-x86-64-linux-gnu_2.34-5 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_8.4.0-3 cpp-9_9.3.0-10 cpp-9-mipsel-linux-gnu_9.3.0-8cross1 cpp-mipsel-linux-gnu_4:9.2.1-4.1 cross-config_2.6.15-3 crossbuild-essential-mipsel_12.8 dash_0.5.10.2-7 debconf_1.5.73 debhelper_12.10 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-10 g++-9-mipsel-linux-gnu_9.3.0-8cross1 g++-mipsel-linux-gnu_4:9.2.1-4.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200402-1 gcc-10-cross-base-mipsen_10-20200324-1cross1 gcc-8-base_8.4.0-3 gcc-9_9.3.0-10 gcc-9-base_9.3.0-10 gcc-9-cross-base-mipsen_9.3.0-8cross1 gcc-9-mipsel-linux-gnu_9.3.0-8cross1 gcc-9-mipsel-linux-gnu-base_9.3.0-8cross1 gcc-mipsel-linux-gnu_4:9.2.1-4.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.0.1 libarchive-zip-perl_1.68-1 libasan5_9.3.0-10 libatomic1_10-20200402-1 libatomic1-mipsel-cross_10-20200324-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-dev-mipsel-cross_2.30-2cross1 libc6-mipsel-cross_2.30-2cross1 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200402-1 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5 libctf0_2.34-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.4.0-3 libgcc-9-dev_9.3.0-10 libgcc-9-dev-mipsel-cross_9.3.0-8cross1 libgcc-s1_10-20200402-1 libgcc-s1-mipsel-cross_10-20200324-1cross1 libgcc1_1:10-20200402-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200402-1 libgomp1-mipsel-cross_10-20200324-1cross1 libgpg-error0_1.37-1 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10-20200402-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200402-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.4.0-3 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 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_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libquadmath0_10-20200402-1 libseccomp2_2.4.3-1 libselinux1_3.0-1+b2 libsemanage-common_3.0-1 libsemanage1_3.0-1+b2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.6-1 libstdc++-8-dev_8.4.0-3 libstdc++-9-dev_9.3.0-10 libstdc++-9-dev-mipsel-cross_9.3.0-8cross1 libstdc++6_10-20200402-1 libstdc++6-mipsel-cross_10-20200324-1cross1 libsub-override-perl_0.09-2 libsystemd0_245.4-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200402-1 libubsan1_10-20200402-1 libuchardet0_0.0.6-3 libudev1_245.4-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-2 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_2.9.10+dfsg-4 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.5.13-2 linux-libc-dev-mipsel-cross_5.4.19-1cross1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 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-2 zlib1g-dev_1:1.2.11.dfsg-2

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


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-3
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: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/plink
Vcs-Git: https://salsa.debian.org/med-team/plink.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), zlib1g-dev
Package-List:
 plink deb science optional arch=any
Checksums-Sha1:
 c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz
 2d96ff7726226a8af98c359f1ad30113d265ce8d 16792 plink_1.07+dfsg-3.debian.tar.xz
Checksums-Sha256:
 e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz
 252c59600d73bd657d97374d8023a7d65b45c3835d98c4ea09082bb19d6ff1f5 16792 plink_1.07+dfsg-3.debian.tar.xz
Files:
 fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz
 3c4f0c4f736d2d55fa5beb712cd09804 16792 plink_1.07+dfsg-3.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 Sun Jan  5 08:03:31 2020 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./plink_1.07+dfsg-3.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-3.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.mipsel
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-0c769f71-a7fc-4923-b08b-b34699544188
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage -amipsel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package plink
dpkg-buildpackage: info: source version 1.07+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-architecture: warning: specified GNU system type mipsel-linux-gnu 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 mipsel
 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>>'
dh_auto_build -- 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 -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mipsel-linux-gnu-pkg-config CXX=mipsel-linux-gnu-g\+\+ CC=mipsel-linux-gnu-gcc "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>>'
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 2366 |     for (int l=0; l<SNP.size(); l++)
      |                   ~^~~~~~~~~~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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) )
      |         ~~~~^~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  398 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  603 |       if ( gn != 2 * sample.size() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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;
      |       ^~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1430:12: warning: ‘maxI’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1430 |    cur[maxI] = false;
      |            ^
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1531 |   for (int i = 0; i < v.size(); i++)
      |                   ~~^~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |       ^
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |        ^~~~~~~
mipsel-linux-gnu-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
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1664 |    for (int i=0;i<tokens.size();i++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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);
      |        ^~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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";
      |                 ~~~~~~~~^~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  105 |    for (int i=0;i<tokens.size();i++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ) );
      |                                                        ~~~~~^~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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;
      |           ^
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  560 |   for (int i=0; i<spec.size(); i++)
      |                 ~^~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1888 |       for (int z = 0; z < h1.size(); z++)
      |                       ~~^~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1245 |    for ( int k=0; k<person->pp->kids.size(); k++)
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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)) ;
      |                                      ~~~^~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘unsigned int’} [-Wsign-compare]
  102 |   for (int l=0; l<snpset.size(); l++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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:805:82: warning: ‘cancor1_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  805 |      gene1[i] += (-1 - mean[j]) * coeff_gene1[order_eigenvalues_gene1[cancor1_pos]][j];
      |                                                                                  ^
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1042 |   for (int i=0; i<snpset.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  273 |      for (int j=0;j< P.pS->snpset[l].size();j++)
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 | }
      | ^
mipsel-linux-gnu-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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  340 |   for (int k=0; k<person->kids.size(); k++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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)
      |   ^~
mipsel-linux-gnu-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 ‘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 ‘unsigned int’} [-Wsign-compare]
  173 |   for (int s=0; s<snpset.size(); s++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  131 |   for (int i=0; i<schi.size(); i++)
      |                 ~^~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ) )
      |                          ~~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |          ^~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  218 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |          ^~
mipsel-linux-gnu-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 ‘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 ‘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) {
      |       ^~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  883 |    for (int i=0; i<sample.size(); i++)
      |                  ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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)
      |      ^~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  373 |        for (int z = 0 ; z < haplo->hap1[i].size(); z++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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:203:18: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  203 |         << start - last - 1 << " ";
      |            ~~~~~~^~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
mipsel-linux-gnu-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 ‘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 ‘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 )
      |              ~~~~~~~~~~~~~^~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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;
      |        ^~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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);
      |                    ~~~~~~~~^~~~~~~~~~
mipsel-linux-gnu-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;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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);
      |     ^~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |           ^~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  209 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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;
      |       ^~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  289 |    for (int i=25; i<tokens.size()-1; i++)
      |                   ~^~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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) << " ";
      |                                                          ^
mipsel-linux-gnu-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 ‘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 ‘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;
      |           ^~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  145 |    for (int z = 0 ; z < hap1[i].size(); z++)
      |                     ~~^~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1666 |       for (int z = 0; z < windows[w]->hap1[r].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  966 |     for (int z2=0; z2<hap1[i].size(); z2++)
      |                    ~~^~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |              ^~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1097 |               if( j < grouped_snps.size()-1)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  358 |    for (int z2=0; z2<new_hap1.size(); z2++)
      |                   ~~^~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  166 |       for (int z=0; z<hap1[i].size(); z++)
      |                     ~^~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  313 |       for (int s=0; s < g.size(); s++)
      |                     ~~^~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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)
      |           ~^~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  667 |   for (int l=0; l<f.size(); l++)
      |                 ~^~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  253 |       else if ( i == s.length()-1 )
      |                 ~~^~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1434 |    if ( cnt>0 && cnt2 < m.group[h].size() )
      |                  ~~~~~^~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |                       ^~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  556 |  for (int i=0; i<sample.size(); i++)
      |                ~^~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ];
      |          ^~~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |       ^~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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;
      |            ^~~~~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  288 |       for (int i = 0 ; i < inds.size() ; i++)
      |                        ~~^~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  196 |       for (int i=0; i < snpset[j].size(); i++)
      |                     ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 2234 |    for (int j = 0 ; j < group->values.size(); j++ )
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  325 |    for (int t = 0 ; t < tokens.size() ; t++)
      |                     ~~^~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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);
      |          ^
mipsel-linux-gnu-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 ‘unsigned int’} [-Wsign-compare]
   73 |        for ( int k = 0 ; k < i->second.size(); k++)
      |                          ~~^~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |                     ^
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |         ^~~~~~~
mipsel-linux-gnu-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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  680 |      for (int f=0; f<par::meta_files.size(); f++)
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
mipsel-linux-gnu-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 Rconnection.h:42,
                 from r.cpp:29:
Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp]
  327 |     #warning using little endian based on information from endian.h
      |      ^~~~~~~
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 ‘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;
      |          ^~
mipsel-linux-gnu-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.h:42,
                 from Rconnection.cpp:30:
Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp]
  327 |     #warning using little endian based on information from endian.h
      |      ^~~~~~~
In file included from 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;
      |                           ^~~~
mipsel-linux-gnu-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
mipsel-linux-gnu-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 
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch
   dh_testroot -a
   dh_prep -a
   dh_installdirs -a
   dh_auto_install -a
   dh_install -a
   dh_installdocs -a
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs debian/upstream.changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
chmod 644 debian/plink/usr/share/doc/plink/examples/*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installman -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-3_mipsel.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-3_mipsel.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any >../plink_1.07+dfsg-3_mipsel.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-04-06T12:09:31Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


plink_1.07+dfsg-3_mipsel.changes:
---------------------------------

Format: 1.8
Date: Sun, 05 Jan 2020 08:27:40 +0100
Source: plink
Binary: plink plink-dbgsym
Built-For-Profiles: cross nocheck
Architecture: mipsel
Version: 1.07+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 plink      - whole-genome association analysis toolset
Closes: 948133
Changes:
 plink (1.07+dfsg-3) unstable; urgency=medium
 .
   [ Helmut Grohne ]
   * Fix FTCBFS: Let dh_auto_build pass cross tools to make. (Closes: #948133)
 .
   [ Andreas Tille ]
   * debhelper-compat 12
   * Standards-Version: 4.4.1
   * Remove obsolete field Name from debian/upstream/metadata (already
     present in machine-readable debian/copyright).
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+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: plink
Binary: plink
Architecture: mipsel
Version: 1.07+dfsg-3
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Mon, 06 Apr 2020 12:09:30 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.69-11.1),
 automake (= 1:1.16.1-4),
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 binutils (= 2.34-5),
 binutils-common (= 2.34-5),
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 bsdutils (= 1:2.34-0.1),
 build-essential (= 12.8),
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 coreutils (= 8.30-3+b1),
 cpp (= 4:9.2.1-3.1),
 cpp-9 (= 9.3.0-10),
 dash (= 0.5.10.2-7),
 debconf (= 1.5.73),
 debhelper (= 12.10),
 debianutils (= 4.9.1),
 dh-autoreconf (= 19),
 dh-strip-nondeterminism (= 1.6.3-2),
 diffutils (= 1:3.7-3),
 dpkg (= 1.19.7),
 dpkg-dev (= 1.19.7),
 dwz (= 0.13-5),
 fdisk (= 2.34-0.1),
 file (= 1:5.38-4),
 findutils (= 4.7.0-1),
 g++ (= 4:9.2.1-3.1),
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 gcc (= 4:9.2.1-3.1),
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 gcc-9-base (= 9.3.0-10),
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 libarchive-zip-perl (= 1.68-1),
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 libbinutils (= 2.34-5),
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 libbsd0 (= 0.10.0-1),
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 make (= 4.2.1-1.2),
 man-db (= 2.9.1-1),
 mawk (= 1.3.4.20200120-2),
 ncurses-base (= 6.2-1),
 ncurses-bin (= 6.2-1),
 patch (= 2.7.6-6),
 perl (= 5.30.0-9),
 perl-base (= 5.30.0-9),
 perl-modules-5.30 (= 5.30.0-9),
 po-debconf (= 1.0.21),
 sed (= 4.7-1),
 sensible-utils (= 0.0.12+nmu1),
 sysvinit-utils (= 2.96-3),
 tar (= 1.30+dfsg-7),
 util-linux (= 2.34-0.1),
 xz-utils (= 5.2.4-1+b1),
 zlib1g (= 1:1.2.11.dfsg-2),
 zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_US.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1578209260"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


plink-dbgsym_1.07+dfsg-3_mipsel.deb
-----------------------------------

 new Debian package, version 2.0.
 size 24223488 bytes: control archive=540 bytes.
     373 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: plink-dbgsym
 Source: plink
 Version: 1.07+dfsg-3
 Auto-Built-Package: debug-symbols
 Architecture: mipsel
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 24042
 Depends: plink (= 1.07+dfsg-3)
 Section: debug
 Priority: optional
 Description: debug symbols for plink
 Build-Ids: a17c143a7835e8bcfccd083e628c24f765ab6aea

drwxr-xr-x root/root         0 2020-01-05 07:27 ./
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root  24607852 2020-01-05 07:27 ./usr/lib/debug/.build-id/a1/7c143a7835e8bcfccd083e628c24f765ab6aea.debug
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/share/doc/plink-dbgsym -> plink


plink_1.07+dfsg-3_mipsel.deb
----------------------------

 new Debian package, version 2.0.
 size 1031452 bytes: control archive=1296 bytes.
    1094 bytes,    26 lines      control              
     915 bytes,    13 lines      md5sums              
 Package: plink
 Version: 1.07+dfsg-3
 Architecture: mipsel
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3865
 Depends: libc6 (>= 2.29), libcrypt1 (>= 1:4.1.0), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
 Recommends: med-config (>= 2.1)
 Section: science
 Priority: optional
 Homepage: http://zzz.bwh.harvard.edu/plink/
 Description: whole-genome association analysis toolset
  plink expects as input the data from SNP (single
  nucleotide polymorphism) chips of many individuals
  and their phenotypical description of a disease.
  It finds associations of single or pairs of DNA
  variations with a phenotype and can retrieve
  SNP annotation from an online source.
  .
  SNPs can evaluated individually or as pairs for their
  association with the disease phenotypes. The joint
  investigation of copy number variations is supported.
  A variety of statistical tests have been implemented.
  .
  Please note: The executable was renamed to plink1
  because of a name clash.  Please read more about this
  in /usr/share/doc/plink/README.Debian.

drwxr-xr-x root/root         0 2020-01-05 07:27 ./
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/bin/
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/bin/p-link -> ../lib/debian-med/bin/plink
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/bin/plink1 -> ../lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/bin/
-rwxr-xr-x root/root   3908436 2020-01-05 07:27 ./usr/lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/share/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/lib/debian-med/share/man/man1/plink.1.gz -> ../../../../../share/man/man1/p-link.1.gz
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/lib/plink/
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/lib/plink/plink -> ../debian-med/bin/plink
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/doc/plink/
-rw-r--r-- root/root       566 2020-01-05 07:27 ./usr/share/doc/plink/NEWS.Debian.gz
-rw-r--r-- root/root      1894 2020-01-05 07:27 ./usr/share/doc/plink/README.Debian
-rw-r--r-- root/root      1287 2007-07-27 14:51 ./usr/share/doc/plink/README.txt
-rw-r--r-- root/root      2365 2020-01-05 07:27 ./usr/share/doc/plink/changelog.Debian.gz
-rw-r--r-- root/root      8639 2020-01-05 07:27 ./usr/share/doc/plink/changelog.gz
-rw-r--r-- root/root      2290 2020-01-05 07:27 ./usr/share/doc/plink/copyright
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/doc/plink/examples/
-rw-r--r-- root/root       358 2020-01-05 07:27 ./usr/share/doc/plink/examples/README
-rw-r--r-- root/root       267 2020-01-05 07:27 ./usr/share/doc/plink/examples/expected.plink.assoc
-rw-r--r-- root/root       126 2020-01-05 07:27 ./usr/share/doc/plink/examples/expected.plink.frq
-rw-r--r-- root/root        23 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.map
-rw-r--r-- root/root       138 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.ped
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/man/
drwxr-xr-x root/root         0 2020-01-05 07:27 ./usr/share/man/man1/
-rw-r--r-- root/root       688 2020-01-05 07:27 ./usr/share/man/man1/p-link.1.gz
lrwxrwxrwx root/root         0 2020-01-05 07:27 ./usr/share/man/man1/plink1.1.gz -> p-link.1.gz


lintian
-------


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

Merged Build-Depends: lintian:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [538 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [626 B]
Fetched 2127 B in 0s (81.2 kB/s)
Reading package lists...
Reading package lists...

Install lintian build dependencies (apt-based resolver)
-------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcpanel-json-xs-perl
  libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl
  libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl
  libhtml-parser-perl libhtml-tagset-perl libimport-into-perl
  libio-async-loop-epoll-perl libio-async-perl libio-pty-perl
  libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl
  libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl
  liblist-moreutils-perl libmailtools-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl
  libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl
  libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl
  libnumber-compare-perl libpackage-stash-perl libparams-classify-perl
  libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl
  libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-name-perl libsub-quote-perl libtext-glob-perl
  libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl
  libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl
  libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils
  perl-openssl-defaults readline-common t1utils
Suggested packages:
  libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl
  libbareword-filehandles-perl libindirect-perl libmultidimensional-perl
  libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl
  binutils-multiarch libtext-template-perl readline-doc
Recommended packages:
  gnupg libhttp-message-perl libasync-mergepoint-perl libsereal-perl
  libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl
  libnet-dns-sec-perl libnet-libidn-perl libperl4-corelibs-perl
  libauthen-sasl-perl libpackage-stash-xs-perl libref-util-perl
  libtype-tiny-xs-perl libperlio-gzip-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcpanel-json-xs-perl
  libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl
  libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl
  libhtml-parser-perl libhtml-tagset-perl libimport-into-perl
  libio-async-loop-epoll-perl libio-async-perl libio-pty-perl
  libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl
  libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl
  liblist-moreutils-perl libmailtools-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl
  libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl
  libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl
  libnumber-compare-perl libpackage-stash-perl libparams-classify-perl
  libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl
  libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-name-perl libsub-quote-perl libtext-glob-perl
  libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl
  libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl
  libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils
  perl-openssl-defaults readline-common
  sbuild-build-depends-lintian-dummy:mipsel t1utils
0 upgraded, 80 newly installed, 0 to remove and 0 not upgraded.
Need to get 9361 kB of archives.
After this operation, 26.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 6.1 [19.9 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-4 [661 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b3 [38.4 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.43-2 [15.0 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.19-1 [126 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b1 [26.0 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1f-1 [1543 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 4 [7148 B]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-3 [320 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.067-1 [212 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3200-1 [39.1 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.23-1 [369 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1 [317 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.44-1 [83.5 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-5 [105 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.75-1 [269 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.017-1 [16.8 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.12-1 [36.3 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004000-1 [12.5 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.011+ds-1 [106 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.011+ds-1 [108 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010001-1 [338 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.81+repack-1 [35.4 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.62.0 [1292 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 20909 files and directories currently installed.)
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Setting up libapt-pkg-perl (0.1.36+b3) ...
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Setting up libclass-method-modifiers-perl (2.13-1) ...
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Setting up libio-pty-perl (1:1.12-1) ...
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Setting up libyaml-0-2:amd64 (0.2.2-1) ...
Setting up libsub-identify-perl (0.14-1+b2) ...
Setting up libcpanel-json-xs-perl (4.19-1) ...
Setting up libssl1.1:amd64 (1.1.1f-1) ...
Setting up libhtml-tagset-perl (3.20-4) ...
Setting up libdevel-size-perl (0.83-1+b1) ...
Setting up libsqlite3-0:amd64 (3.31.1-4) ...
Setting up libfuture-perl (0.44-1) ...
Setting up libyaml-libyaml-perl (0.81+repack-1) ...
Setting up libtry-tiny-perl (0.30-1) ...
Setting up perl-openssl-defaults:amd64 (4) ...
Setting up libtext-levenshtein-perl (0.13-1) ...
Setting up libassuan0:amd64 (2.5.3-7) ...
Setting up libsereal-encoder-perl (4.011+ds-1) ...
Setting up libnumber-compare-perl (0.03-1) ...
Setting up libio-async-perl (0.75-1) ...
Setting up patchutils (0.3.4-2+b1) ...
Setting up libjson-maybexs-perl (1.004000-1) ...
Setting up libfile-find-rule-perl (0.34-1) ...
Setting up libdigest-hmac-perl (1.03+dfsg-2) ...
Setting up libipc-system-simple-perl (1.30-1) ...
Setting up libnet-domain-tld-perl (1.75-1) ...
Setting up libxml-writer-perl (0.625-1) ...
Setting up t1utils (1.41-3) ...
Setting up liblinux-epoll-perl (0.017-1) ...
Setting up diffstat (1.63-1) ...
Setting up libvariable-magic-perl (0.62-1+b2) ...
Setting up libb-hooks-op-check-perl (0.22-1+b2) ...
Setting up libipc-run-perl (20180523.0-2) ...
Setting up libsub-exporter-progressive-perl (0.001013-1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3200-1) ...
Setting up libsub-name-perl (0.26-1) ...
Setting up libpath-tiny-perl (0.108-1) ...
Setting up librole-tiny-perl (2.001004-1) ...
Setting up netbase (6.1) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006006-1) ...
Setting up libclass-xsaccessor-perl (1.19-3+b3) ...
Setting up libexporter-tiny-perl (1.002001-1) ...
Setting up libfont-ttf-perl (1.06-1) ...
Setting up libnet-ip-perl (1.26-2) ...
Setting up readline-common (8.0-4) ...
Setting up libsereal-decoder-perl (4.011+ds-1) ...
Setting up liburi-perl (1.76-2) ...
Setting up libnet-ssleay-perl (1.88-3) ...
Setting up libfile-basedir-perl (0.08-1) ...
Setting up liblist-moreutils-perl (0.416-1+b5) ...
Setting up libreadline8:amd64 (8.0-4) ...
Setting up libtype-tiny-perl (1.010001-1) ...
Setting up libnet-dns-perl (1.23-1) ...
Setting up libdevel-callchecker-perl (0.008-1+b1) ...
Setting up libio-async-loop-epoll-perl (0.20-1) ...
Setting up libhtml-parser-perl (3.72-5) ...
Setting up gpgconf (2.2.20-1) ...
Setting up libio-socket-ssl-perl (2.067-1) ...
Setting up gpg (2.2.20-1) ...
Setting up libparams-classify-perl (0.015-1+b2) ...
Setting up libnet-smtp-ssl-perl (1.04-1) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libmailtools-perl (2.21-1) ...
Setting up libmodule-implementation-perl (0.09-1) ...
Setting up libemail-valid-perl (1.202-1) ...
Setting up libpackage-stash-perl (0.38-1) ...
Setting up libimport-into-perl (1.002005-1) ...
Setting up libmoo-perl (2.003006-1) ...
Setting up libmoox-aliases-perl (0.001006-1) ...
Setting up libb-hooks-endofscope-perl (0.24-1) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.62.0) ...
Setting up sbuild-build-depends-lintian-dummy:mipsel (0.invalid.0) ...
Processing triggers for man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.30-4) ...

I: Lintian run was successful.

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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 357020
Build-Time: 532
Distribution: unstable
Foreign Architectures: mipsel
Host Architecture: mipsel
Install-Time: 17
Job: plink_1.07+dfsg-3
Lintian: pass
Machine Architecture: amd64
Package: plink
Package-Time: 559
Source-Version: 1.07+dfsg-3
Space: 357020
Status: successful
Version: 1.07+dfsg-3
--------------------------------------------------------------------------------
Finished at 2020-04-06T12:09:31Z
Build needed 00:09:19, 357020k disk space