sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir

+==============================================================================+
| plink 1.07+dfsg-4 (i386)                     Tue, 05 Apr 2022 21:37:58 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-4
Source Version: 1.07+dfsg-4
Distribution: unstable
Machine Architecture: arm64
Host Architecture: i386
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-7b32d804-4874-4ec2-b7ec-f537740885a2' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-tIzykU/resolver-WX2tka' with '<<RESOLVERDIR>>'

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

Get:1 http://mirror.einval.org/debian sid InRelease [165 kB]
Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index
Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index
Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB]
Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index
Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index
Get:4 http://mirror.einval.org/debian sid/main i386 Packages [9036 kB]
Get:5 http://mirror.einval.org/debian sid/main Sources [9673 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8984 kB]
Fetched 27.9 MB in 7s (3785 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 449 kB of source archives.
Get:1 http://mirror.einval.org/debian sid/main plink 1.07+dfsg-4 (dsc) [2076 B]
Get:2 http://mirror.einval.org/debian sid/main plink 1.07+dfsg-4 (tar) [429 kB]
Get:3 http://mirror.einval.org/debian sid/main plink 1.07+dfsg-4 (diff) [17.4 kB]
Fetched 449 kB in 0s (8428 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-tIzykU/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-tIzykU' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386
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 [411 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [499 B]
Fetched 1867 B in 0s (44.2 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-i686-linux-gnu
  bsdextrautils cpp-11-i686-linux-gnu cpp-i686-linux-gnu cross-config
  crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu
  gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu
  gcc-11-i686-linux-gnu-base gcc-12-base:i386 gcc-12-cross-base
  gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386
  libatomic1-i386-cross libc6:i386 libc6-dev:i386 libc6-dev-i386-cross
  libc6-i386-cross libcom-err2:i386 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:i386
  libgcc-11-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386
  libgomp1-i386-cross libgssapi-krb5-2:i386 libicu67 libio-string-perl
  libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386
  libkrb5-3:i386 libkrb5support0:i386 liblocale-gettext-perl libmagic-mgc
  libmagic1 libnsl-dev:i386 libnsl2:i386 libpipeline1 libquadmath0:i386
  libquadmath0-i386-cross libsigsegv2 libssl1.1:i386 libstdc++-11-dev:i386
  libstdc++-11-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross
  libsub-override-perl libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386
  libubsan1-i386-cross libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386
  linux-libc-dev-i386-cross m4 man-db po-debconf sensible-utils ucf
  zlib1g:i386 zlib1g-dev:i386
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales
  cpp-doc dh-make binutils-multiarch g++-11-multilib-i686-linux-gnu gcc-11-doc
  gcc-11-multilib-i686-linux-gnu manpages-dev flex bison gdb-i686-linux-gnu
  gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:i386
  libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386
  manpages-dev:i386 krb5-doc:i386 krb5-user:i386 libstdc++-11-doc:i386
  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:i386 libarchive-cpio-perl krb5-locales:i386
  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-i686-linux-gnu
  bsdextrautils cpp-11-i686-linux-gnu cpp-i686-linux-gnu cross-config
  crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu
  gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu
  gcc-11-i686-linux-gnu-base gcc-12-base:i386 gcc-12-cross-base
  gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386
  libatomic1-i386-cross libc6:i386 libc6-dev:i386 libc6-dev-i386-cross
  libc6-i386-cross libcom-err2:i386 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:i386
  libgcc-11-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386
  libgomp1-i386-cross libgssapi-krb5-2:i386 libicu67 libio-string-perl
  libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386
  libkrb5-3:i386 libkrb5support0:i386 liblocale-gettext-perl libmagic-mgc
  libmagic1 libnsl-dev:i386 libnsl2:i386 libpipeline1 libquadmath0:i386
  libquadmath0-i386-cross libsigsegv2 libssl1.1:i386 libstdc++-11-dev:i386
  libstdc++-11-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross
  libsub-override-perl libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386
  libubsan1-i386-cross libuchardet0 libxml-libxml-perl
  libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl
  libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386
  linux-libc-dev-i386-cross m4 man-db po-debconf
  sbuild-build-depends-main-dummy:i386 sensible-utils ucf zlib1g:i386
  zlib1g-dev:i386
0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded.
Need to get 85.9 MB of archives.
After this operation, 329 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://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b2 [18.9 kB]
Get:3 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB]
Get:4 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.41-3 [295 kB]
Get:5 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.41-3 [124 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.41-3 [66.9 kB]
Get:7 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-6 [173 kB]
Get:8 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get:9 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-8 [882 kB]
Get:10 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.3-1+b1 [145 kB]
Get:11 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.5-1 [35.8 kB]
Get:12 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.10.2-1 [1392 kB]
Get:13 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB]
Get:14 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.14-1 [37.0 kB]
Get:15 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get:16 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB]
Get:17 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:18 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:19 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-6 [510 kB]
Get:20 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu-base arm64 11.2.0-18cross1 [208 kB]
Get:21 http://mirror.einval.org/debian sid/main arm64 cpp-11-i686-linux-gnu arm64 11.2.0-18cross1 [7859 kB]
Get:22 http://mirror.einval.org/debian sid/main arm64 cpp-i686-linux-gnu arm64 4:11.2.0-2 [17.0 kB]
Get:23 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB]
Get:24 http://mirror.einval.org/debian sid/main arm64 binutils-i686-linux-gnu arm64 2.38-3 [2321 kB]
Get:25 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-18cross1 [203 kB]
Get:26 http://mirror.einval.org/debian sid/main arm64 gcc-12-cross-base all 12-20220222-1cross1 [202 kB]
Get:27 http://mirror.einval.org/debian sid/main arm64 libc6-i386-cross all 2.33-1cross1 [1526 kB]
Get:28 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-i386-cross all 12-20220222-1cross1 [60.3 kB]
Get:29 http://mirror.einval.org/debian sid/main arm64 libgomp1-i386-cross all 12-20220222-1cross1 [118 kB]
Get:30 http://mirror.einval.org/debian sid/main arm64 libitm1-i386-cross all 12-20220222-1cross1 [27.2 kB]
Get:31 http://mirror.einval.org/debian sid/main arm64 libatomic1-i386-cross all 12-20220222-1cross1 [7492 B]
Get:32 http://mirror.einval.org/debian sid/main arm64 libasan6-i386-cross all 11.2.0-18cross1 [1927 kB]
Get:33 http://mirror.einval.org/debian sid/main arm64 libstdc++6-i386-cross all 12-20220222-1cross1 [622 kB]
Get:34 http://mirror.einval.org/debian sid/main arm64 libubsan1-i386-cross all 12-20220222-1cross1 [867 kB]
Get:35 http://mirror.einval.org/debian sid/main arm64 libquadmath0-i386-cross all 12-20220222-1cross1 [225 kB]
Get:36 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-i386-cross all 11.2.0-18cross1 [2331 kB]
Get:37 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu arm64 11.2.0-18cross1 [15.6 MB]
Get:38 http://mirror.einval.org/debian sid/main arm64 gcc-i686-linux-gnu arm64 4:11.2.0-2 [1452 B]
Get:39 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-i386-cross all 5.15.5-1cross1 [1576 kB]
Get:40 http://mirror.einval.org/debian sid/main arm64 libc6-dev-i386-cross all 2.33-1cross1 [2170 kB]
Get:41 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-i386-cross all 11.2.0-18cross1 [2012 kB]
Get:42 http://mirror.einval.org/debian sid/main arm64 g++-11-i686-linux-gnu arm64 11.2.0-18cross1 [8676 kB]
Get:43 http://mirror.einval.org/debian sid/main arm64 g++-i686-linux-gnu arm64 4:11.2.0-2 [1168 B]
Get:44 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
Get:45 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB]
Get:46 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get:47 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.13+dfsg-1 [641 kB]
Get:48 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB]
Get:49 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB]
Get:50 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:51 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1 [326 kB]
Get:52 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:53 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB]
Get:54 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB]
Get:55 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:56 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB]
Get:57 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB]
Get:58 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB]
Get:59 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-i386 all 12.9 [6704 B]
Get:60 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.6 [193 kB]
Get:61 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.7-2 [526 kB]
Get:62 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:63 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:64 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:65 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:66 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:67 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.186-1 [177 kB]
Get:68 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB]
Get:69 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-6 [1260 kB]
Get:70 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:71 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:72 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.6 [1054 kB]
Get:73 http://mirror.einval.org/debian sid/main i386 gcc-11-base i386 11.2.0-19 [208 kB]
Get:74 http://mirror.einval.org/debian sid/main i386 gcc-12-base i386 12-20220319-1 [206 kB]
Get:75 http://mirror.einval.org/debian sid/main i386 libgcc-s1 i386 12-20220319-1 [60.0 kB]
Get:76 http://mirror.einval.org/debian sid/main i386 libc6 i386 2.33-7 [2790 kB]
Get:77 http://mirror.einval.org/debian sid/main i386 libasan6 i386 11.2.0-19 [1934 kB]
Get:78 http://mirror.einval.org/debian sid/main i386 libatomic1 i386 12-20220319-1 [7704 B]
Get:79 http://mirror.einval.org/debian sid/main i386 linux-libc-dev i386 5.16.18-1 [1517 kB]
Get:80 http://mirror.einval.org/debian sid/main i386 libcrypt1 i386 1:4.4.27-1.1 [99.5 kB]
Get:81 http://mirror.einval.org/debian sid/main i386 libcrypt-dev i386 1:4.4.27-1.1 [129 kB]
Get:82 http://mirror.einval.org/debian sid/main i386 libcom-err2 i386 1.46.5-2 [76.1 kB]
Get:83 http://mirror.einval.org/debian sid/main i386 libkrb5support0 i386 1.19.2-2+b1 [69.0 kB]
Get:84 http://mirror.einval.org/debian sid/main i386 libk5crypto3 i386 1.19.2-2+b1 [117 kB]
Get:85 http://mirror.einval.org/debian sid/main i386 libkeyutils1 i386 1.6.1-3 [16.0 kB]
Get:86 http://mirror.einval.org/debian sid/main i386 libssl1.1 i386 1.1.1n-1 [1552 kB]
Get:87 http://mirror.einval.org/debian sid/main i386 libkrb5-3 i386 1.19.2-2+b1 [391 kB]
Get:88 http://mirror.einval.org/debian sid/main i386 libgssapi-krb5-2 i386 1.19.2-2+b1 [177 kB]
Get:89 http://mirror.einval.org/debian sid/main i386 libtirpc3 i386 1.3.2-2 [91.3 kB]
Get:90 http://mirror.einval.org/debian sid/main i386 libnsl2 i386 1.3.0-2 [42.2 kB]
Get:91 http://mirror.einval.org/debian sid/main i386 libtirpc-dev i386 1.3.2-2 [201 kB]
Get:92 http://mirror.einval.org/debian sid/main i386 libnsl-dev i386 1.3.0-2 [70.6 kB]
Get:93 http://mirror.einval.org/debian sid/main i386 libc6-dev i386 2.33-7 [2172 kB]
Get:94 http://mirror.einval.org/debian sid/main i386 libgomp1 i386 12-20220319-1 [121 kB]
Get:95 http://mirror.einval.org/debian sid/main i386 libitm1 i386 12-20220319-1 [27.7 kB]
Get:96 http://mirror.einval.org/debian sid/main i386 libstdc++6 i386 12-20220319-1 [664 kB]
Get:97 http://mirror.einval.org/debian sid/main i386 libubsan1 i386 12-20220319-1 [870 kB]
Get:98 http://mirror.einval.org/debian sid/main i386 libquadmath0 i386 12-20220319-1 [227 kB]
Get:99 http://mirror.einval.org/debian sid/main i386 libgcc-11-dev i386 11.2.0-19 [2331 kB]
Get:100 http://mirror.einval.org/debian sid/main i386 libstdc++-11-dev i386 11.2.0-19 [2007 kB]
Get:101 http://mirror.einval.org/debian sid/main i386 zlib1g i386 1:1.2.11.dfsg-4 [93.0 kB]
Get:102 http://mirror.einval.org/debian sid/main i386 zlib1g-dev i386 1:1.2.11.dfsg-4 [194 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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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...

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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...
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Setting up libxml-simple-perl (2.25-1) ...
Setting up libgcc-11-dev-i386-cross (11.2.0-18cross1) ...
Setting up libconfig-auto-perl (0.44-1.1) ...
Setting up gcc-11-i686-linux-gnu (11.2.0-18cross1) ...
Setting up gcc-i686-linux-gnu (4:11.2.0-2) ...
Setting up libstdc++-11-dev-i386-cross (11.2.0-18cross1) ...
Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ...
Setting up g++-11-i686-linux-gnu (11.2.0-18cross1) ...
Setting up dpkg-cross (2.6.18+nmu2) ...
Setting up g++-i686-linux-gnu (4:11.2.0-2) ...
Setting up crossbuild-essential-i386 (12.9) ...
Setting up libgcc-s1:i386 (12-20220319-1) ...
Setting up libc6:i386 (2.33-7) ...
Setting up libstdc++6:i386 (12-20220319-1) ...
Setting up libitm1:i386 (12-20220319-1) ...
Setting up libkeyutils1:i386 (1.6.1-3) ...
Setting up libssl1.1:i386 (1.1.1n-1) ...
Setting up zlib1g:i386 (1:1.2.11.dfsg-4) ...
Setting up libcrypt1:i386 (1:4.4.27-1.1) ...
Setting up libcom-err2:i386 (1.46.5-2) ...
Setting up libgomp1:i386 (12-20220319-1) ...
Setting up libasan6:i386 (11.2.0-19) ...
Setting up libkrb5support0:i386 (1.19.2-2+b1) ...
Setting up libquadmath0:i386 (12-20220319-1) ...
Setting up libatomic1:i386 (12-20220319-1) ...
Setting up libk5crypto3:i386 (1.19.2-2+b1) ...
Setting up libubsan1:i386 (12-20220319-1) ...
Setting up libgcc-11-dev:i386 (11.2.0-19) ...
Setting up libcrypt-dev:i386 (1:4.4.27-1.1) ...
Setting up libkrb5-3:i386 (1.19.2-2+b1) ...
Setting up libgssapi-krb5-2:i386 (1.19.2-2+b1) ...
Setting up libtirpc3:i386 (1.3.2-2) ...
Setting up libtirpc-dev:i386 (1.3.2-2) ...
Setting up libnsl2:i386 (1.3.0-2) ...
Setting up libnsl-dev:i386 (1.3.0-2) ...
Setting up libc6-dev:i386 (2.33-7) ...
Setting up libstdc++-11-dev:i386 (11.2.0-19) ...
Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-4) ...
Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7) ...

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

Arch check ok (i386 included in any)

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

Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64)
Toolchain package versions: binutils_2.38-3 dpkg-dev_1.21.7 g++-11_11.2.0-19 gcc-11_11.2.0-19 libc6-dev_2.33-7 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-i386-cross_11.2.0-18cross1 libstdc++6_12-20220319-1 libstdc++6-i386-cross_12-20220222-1cross1 linux-libc-dev_5.16.18-1
Package versions: adduser_3.121 apt_2.4.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3 binutils-aarch64-linux-gnu_2.38-3 binutils-common_2.38-3 binutils-i686-linux-gnu_2.38-3 bsdextrautils_2.37.3-1+b1 bsdutils_1:2.37.3-1+b1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-19 cpp-11-i686-linux-gnu_11.2.0-18cross1 cpp-i686-linux-gnu_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-i386_12.9 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.6 debian-archive-keyring_2021.1.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dpkg_1.21.7 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.7 dwz_0.14-1 fakeroot_1.28-1 file_1:5.41-3 findutils_4.9.0-2 g++_4:11.2.0-2 g++-11_11.2.0-19 g++-11-i686-linux-gnu_11.2.0-18cross1 g++-i686-linux-gnu_4:11.2.0-2 gcc_4:11.2.0-2 gcc-11_11.2.0-19 gcc-11-base_11.2.0-19 gcc-11-cross-base_11.2.0-18cross1 gcc-11-i686-linux-gnu_11.2.0-18cross1 gcc-11-i686-linux-gnu-base_11.2.0-18cross1 gcc-12-base_12-20220319-1 gcc-12-cross-base_12-20220222-1cross1 gcc-i686-linux-gnu_4:11.2.0-2 gettext_0.21-6 gettext-base_0.21-6 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.4 libarchive-zip-perl_1.68-1 libasan6_11.2.0-19 libasan6-i386-cross_11.2.0-18cross1 libatomic1_12-20220319-1 libatomic1-i386-cross_12-20220222-1cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3 libblkid1_2.37.3-1+b1 libbz2-1.0_1.0.8-5 libc-bin_2.33-7 libc-dev-bin_2.33-7 libc6_2.33-7 libc6-dev_2.33-7 libc6-dev-i386-cross_2.33-1cross1 libc6-i386-cross_2.33-1cross1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1 libcom-err2_1.46.5-2 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3 libctf0_2.38-3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.21.7 libelf1_0.186-1 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.13.0-1 libfile-which-perl_1.23-1 libgcc-11-dev_11.2.0-19 libgcc-11-dev-i386-cross_11.2.0-18cross1 libgcc-s1_12-20220319-1 libgcc-s1-i386-cross_12-20220222-1cross1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4+b1 libgomp1_12-20220319-1 libgomp1-i386-cross_12-20220222-1cross1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b1 libhogweed6_3.7.3-1 libhwasan0_12-20220319-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl23_0.24-2 libitm1_12-20220319-1 libitm1-i386-cross_12-20220222-1cross1 libk5crypto3_1.19.2-2+b1 libkeyutils1_1.6.1-3 libkrb5-3_1.19.2-2+b1 libkrb5support0_1.19.2-2+b1 liblocale-gettext-perl_1.07-4+b2 liblsan0_12-20220319-1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-3 libmagic1_1:5.41-3 libmount1_2.37.3-1+b1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-14 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libquadmath0_12-20220319-1 libquadmath0-i386-cross_12-20220222-1cross1 libseccomp2_2.5.3-2 libselinux1_3.3-1+b2 libsemanage-common_3.3-1 libsemanage2_3.3-1+b2 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1+b1 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-i386-cross_11.2.0-18cross1 libstdc++6_12-20220319-1 libstdc++6-i386-cross_12-20220222-1cross1 libsub-override-perl_0.09-2 libsystemd0_250.4-1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-2 libtsan0_11.2.0-19 libubsan1_12-20220319-1 libubsan1-i386-cross_12-20220222-1cross1 libuchardet0_0.0.7-1 libudev1_250.4-1 libunistring2_1.0-1 libuuid1_2.37.3-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.13+dfsg-1 libxxhash0_0.8.1-1 libyaml-perl_1.30-1 libzstd1_1.4.10+dfsg-1 linux-libc-dev_5.16.18-1 linux-libc-dev-i386-cross_5.15.5-1cross1 login_1:4.11.1+dfsg1-2 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.37.3-1+b1 ncurses-base_6.3-2 ncurses-bin_6.3-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.34_5.34.0-3 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2022a-1 ucf_3.0043 util-linux_2.37.3-1+b1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4

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


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

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

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-4
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 <daissi@debian.org>
Homepage: http://zzz.bwh.harvard.edu/plink/
Standards-Version: 4.6.0
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 (= 13), zlib1g-dev
Package-List:
 plink deb science optional arch=any
Checksums-Sha1:
 c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz
 30da84e59157c428d54473d7e242e394a2dc6aaf 17356 plink_1.07+dfsg-4.debian.tar.xz
Checksums-Sha256:
 e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz
 9cf0a2845eb96c95ed85347bdaf8afcc7bb0c933c960ce2adde2026ec78084c4 17356 plink_1.07+dfsg-4.debian.tar.xz
Files:
 fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz
 d4701d1cd62de5c466ad92f54f17c8c8 17356 plink_1.07+dfsg-4.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.pVf3Bajc/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 31 15:36:45 2021 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./plink_1.07+dfsg-4.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-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 30_endiandetection.patch
dpkg-source: info: applying gcc-4.7.patch
dpkg-source: info: applying Fix_spelling_error.patch
dpkg-source: info: applying gcc11.patch

Check disk space
----------------

Sufficient free space for build

+------------------------------------------------------------------------------+
| Starting Timed Build Commands                                                |
+------------------------------------------------------------------------------+


ulimit -c
---------

0

I: Finished running 'ulimit -c'.

Finished processing commands.
--------------------------------------------------------------------------------

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.i386
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmutg
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=crossqa-sid
SCHROOT_CHROOT_NAME=crossqa-sid
SCHROOT_COMMAND=env
SCHROOT_GID=1002
SCHROOT_GROUP=helmutg
SCHROOT_SESSION_ID=crossqa-sid-7b32d804-4874-4ec2-b7ec-f537740885a2
SCHROOT_UID=1002
SCHROOT_USER=helmutg
SHELL=/bin/sh
USER=helmutg

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

Command: dpkg-buildpackage -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package plink
dpkg-buildpackage: info: source version 1.07+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-architecture: warning: specified GNU system type i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 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 binary-arch
dh binary-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  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc "CXXFLAGS=-Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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>>'
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                   ~^~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:516:22: 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:521:22: 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:545:19: 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:821:32: 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:927:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:1261:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 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:1519:26: 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:1602:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1602 |           for (int i=0;i<tokens.size(); i++)
      |                        ~^~~~~~~~~~~~~~
input.cpp:1745:26: 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:91:20: warning: ‘PED’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   91 |           if ( feof(PED) )
      |                ~~~~^~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:261:19: 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:339:23: 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:351:34: 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++)
      |                    ~~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:591:18: 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() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:99:15: warning: unused variable ‘geno_nm’ [-Wunused-variable]
   99 |           int geno_nm = 0;
      |               ^~~~~~~
genome.cpp:81:14: warning: unused variable ‘tothet’ [-Wunused-variable]
   81 |       double tothet = 0;
      |              ^~~~~~
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:1067:30: 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;
      |       ^~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:267:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:309:15: 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:1389:26: 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:1391:30: 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+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:1477:28: 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++)
      |                   ~~^~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:95:26: 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:123:25: 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:132:30: 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:155:25: 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:163:30: 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:198:25: 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:273:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:762:31: 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:1078:30: 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:1091:30: 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:1165:31: 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;
      |       ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |        ^~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:452:33: 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:511:33: 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:492:15: warning: unused variable ‘size’ [-Wunused-variable]
  492 |           int size = peeps.size();
      |               ^~~~
cluster.cpp:626:29: 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:648:31: 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:651:33: 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:786:25: 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:919:23: 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:955:24: 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:975:26: 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:976:30: 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:990:55: 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:1038:24: 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:1041:40: 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:1049:26: 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:1050:28: 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:1060:28: 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:1061:30: 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:1107:26: 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:1110:30: 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:1133:26: 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:1169:26: 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:1664:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1664 |           for (int i=0;i<tokens.size();i++)
      |                        ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:190:34: 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:191:36: 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);
      |        ^~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:89:26: 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:526:30: 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:144:61: 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:145:61: 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:69:32: warning: ‘i1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   69 |          << setw(6) << genotype(*this,i1,l) << "\n";
      |                        ~~~~~~~~^~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:105:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  105 |           for (int i=0;i<tokens.size();i++)
      |                        ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:395:26: 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:741:28: 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:744:24: 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:788:25: 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:1108:11: warning: ‘pvalue’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1108 |           if ( pvalue <= par::set_score_p && pvalue >= 0 )
      |           ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:154:25: 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:161:25: 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:438:26: warning: unused variable ‘zero’ [-Wunused-variable]
  438 |                   double zero = 0;
      |                          ^~~~
epi.cpp:701:11: warning: unused variable ‘c’ [-Wunused-variable]
  701 |       int c=0;
      |           ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:226:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  226 |               if (len != tokens.size() - offset )
      |                   ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
prephap.cpp:283:44: 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:412:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  412 |           while ( index < tokens.size() )
      |                   ~~~~~~^~~~~~~~~~~~~~~
prephap.cpp:416:41: 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:420:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  420 |               if ( index == tokens.size() - 1 )
      |                    ~~~~~~^~~~~~~~~~~~~~~~~~~~
prephap.cpp:470:25: 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++)
      |                 ~^~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:373:30: 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:678:38: 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:1238:26: 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:1280:30: 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:1299:26: 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:1575:39: 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++)
      |                       ~~^~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:258:30: 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:272:30: 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:335:33: 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:342:31: 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:350:31: 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:504:26: 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:895:30: 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:931:13: warning: unused variable ‘tmp’ [-Wunused-variable]
  931 |         int tmp = deleteSNPs(mendel_locus);
      |             ^~~
trio.cpp:936:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  936 |       for (int f=0;f<family.size();f++)
      |                    ~^~~~~~~~~~~~~~
trio.cpp:943:30: 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:962:13: 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:1236:27: 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:1245:27: 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++)
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:81:26: 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:96:30: 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:144:27: 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:210:26: 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:327:28: 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:330:24: 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:415:25: 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:557:26: 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:668:26: 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:776:26: 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:936:55: warning: ‘zt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  936 |                   double OR_lower = exp( log(OR) - zt * sqrt(1/t1+1/t2)) ;
      |                                                    ~~~^~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                 ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:489:28: 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:497:28: 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:506:17: warning: unused variable ‘n12’ [-Wunused-variable]
  506 |             int n12 = n1 + n2;
      |                 ^~~
genepi.cpp:507:17: 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:1025:28: 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:1033:28: 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:1043:17: warning: unused variable ‘n12’ [-Wunused-variable]
 1043 |             int n12 = n1 + n2;
      |                 ^~~
genepi.cpp:1044:17: warning: unused variable ‘ne’ [-Wunused-variable]
 1044 |             int ne = n1 < n2 ? n1 : n2;// ne = min(p,q)
      |                 ^~
genepi.cpp:1064:17: warning: unused variable ‘nind’ [-Wunused-variable]
 1064 |             int nind = calcGENEPIMeanVariance(pSNP,
      |                 ^~~~
genepi.cpp: In function ‘int calcGENEPIMeanVariance(std::vector<CSNP*>&, int, int, bool, Plink*, std::vector<double>&, std::vector<std::vector<double> >&, std::vector<Individual*>&, std::vector<int>&, std::vector<int>&)’:
genepi.cpp:1198:8: warning: unused variable ‘casewise_deletion’ [-Wunused-variable]
 1198 |   bool casewise_deletion = false;
      |        ^~~~~~~~~~~~~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:855:105: warning: ‘cancor1_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  855 |                             gene2[i] += (-1 - mean[j]) * coeff_gene2[order_eigenvalues_gene2[cancor1_pos]][cur_snp];
      |                                                                                                         ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:59:33: 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:62:48: 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:332:29: 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:370:27: 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:619:23: 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:632:23: 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:643:23: 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:975:26: 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++)
      |                 ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:273:41: 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++)
      |                                        ~^~~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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 | }
      | ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:722:18: 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:842:26: 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)
      |   ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                 ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                 ~^~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:48:34: 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:62:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   62 |                   if ( ! ( haploid || X && person->sex ) )
      |                                       ~~^~~~~~~~~~~~~~
haploCC.cpp:79:34: 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:93:41: 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:340:35: 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:357:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  357 |                   if ( ! ( haploid || X && person->sex ) )
      |                                       ~~^~~~~~~~~~~~~~
haploCC.cpp:375:35: 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:392:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  392 |                    if ( ! ( haploid || X && person->sex ) )
      |                                        ~~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                     ~^~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:198:25: 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:328:26: 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;
      |          ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:130:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  130 |           if ( i < tokens.size()-1 )
      |                ~~^~~~~~~~~~~~~~~~~
webcheck.cpp:146:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  146 |           if ( i < tokens.size()-1 )
      |                ~~^~~~~~~~~~~~~~~~~
webcheck.cpp:180:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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++)
      |                 ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:82:31: 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:89:31: 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:97:31: 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:505:34: 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:648:25: 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:657:25: 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;
      |          ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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) {
      |       ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:883:26: 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++)
      |                         ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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)
      |      ^~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:209:42: 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:236:42: 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:349:34: 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:373:34: 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++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:384:25: 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:461:24: 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:462:26: 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:206:65: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  206 |                       << (double)( locus[start]->bp - locus[last]->bp ) / 1000.0
      |                                                                 ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:861:27: 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:1178:38: 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:1437:27: 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:1441:47: 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:1461:27: 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:2155:27: warning: value computed is not used [-Wunused-value]
 2155 |         homozygWindows[l] == 0;
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:871:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  871 |         if (!ibd)
      |         ^~
segment.cpp:875:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  875 |           SIBS << setw(10) << original[l]  << " "
      |           ^~~~
segment.cpp: In member function ‘void Plink::testGenomeIBDByCovariate(Perm&)’:
segment.cpp:954:22: warning: unused variable ‘p1’ [-Wunused-variable]
  954 |         Individual * p1 = sample[i1];
      |                      ^~
segment.cpp:955:22: warning: unused variable ‘p2’ [-Wunused-variable]
  955 |         Individual * p2 = sample[i2];
      |                      ^~
segment.cpp:1027:26: warning: unused variable ‘p1’ [-Wunused-variable]
 1027 |             Individual * p1 = sample[i1];
      |                          ^~
segment.cpp:1028:26: warning: unused variable ‘p2’ [-Wunused-variable]
 1028 |             Individual * p2 = sample[i2];
      |                          ^~
segment.cpp:950:7: warning: unused variable ‘c’ [-Wunused-variable]
  950 |   int c=0;
      |       ^
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:1855:21: 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:2378:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2378 |           else if ( par::cnv_col = 1 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2380:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2380 |           else if ( par::cnv_col = 2 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2382:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2382 |           else if ( par::cnv_col = 3 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2412:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2412 |           else if ( par::cnv_col = 1 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2414:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2414 |           else if ( par::cnv_col = 2 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2416:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2416 |           else if ( par::cnv_col = 3 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2443:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2443 |           else if ( par::cnv_col = 1 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2445:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2445 |           else if ( par::cnv_col = 2 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2447:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2447 |           else if ( par::cnv_col = 3 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2474:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2474 |           else if ( par::cnv_col = 1 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2476:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2476 |           else if ( par::cnv_col = 2 )
      |                     ~~~~~~~~~~~~~^~~
segment.cpp:2478:34: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 2478 |           else if ( par::cnv_col = 3 )
      |                     ~~~~~~~~~~~~~^~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:374:31: 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");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |        ^~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:294:27: 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:344:30: 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:355:30: 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:423:26: 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:610:35: warning: ‘df’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  610 |           double pvalue = chiprobP(chisq,df);
      |                           ~~~~~~~~^~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:1154:15: warning: ‘p_gcnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1154 |               ++(*p_gcnt);
      |               ^~~~~~~~~~~
elf.cpp:1165:19: warning: ‘p_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1165 |                   ++(*p_cnt);
      |                   ^~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:106:28: 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:239:25: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  239 |               if ( pat1 && (!pat2) ||
      |                    ~~~~~^~~~~~~~~~
dfam.cpp:271:30: 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:378:30: 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:218:16: warning: unused variable ‘informative’ [-Wunused-variable]
  218 |           bool informative = false;
      |                ^~~~~~~~~~~
dfam.cpp:504:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<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;
      |           ^~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:267:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  267 |           prterr(2, "All elements of TABLE must be positive.");
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:272:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  272 |       prterr(3, "All elements of TABLE are zero.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  273 |              "PRT and PRE are set to missing values.");
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f2xact(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, int*, int*, double*)’:
fisher.cpp:448:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  448 |     prterr(1, "NROW must be less than or equal to LDTABL.");
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:450:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  450 |     prterr(4, "NCOL must be at least 2");
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:449:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  449 |   if (*ncol <= 1)
      |   ^~
fisher.cpp:453:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  453 |     for (i = 1; i <= *ldkey << 1; ++i) {
      |     ^~~
fisher.cpp:501:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  501 |               prterr(2, "All elements of TABLE must be positive.");
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:508:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  508 |       prterr(3, "All elements of TABLE are zero.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  509 |                     "PRT and PRE are set to missing values.");
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:559:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  559 |       prterr(5, "The hash table key cannot be computed because "
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  560 |                     "the largest key\n"
      |                     ~~~~~~~~~~~~~~~~~~~
  561 |                     "is larger than the largest representable int.\n"
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  562 |                     "The algorithm cannot proceed.\n"
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  563 |                     "Reduce the workspace size, or use `exact = FALSE'.");
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:750:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  750 |       prterr(6, "LDKEY is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  751 |                     "Try increasing the size of the workspace.");
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void f5xact(double*, const double*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*)’:
fisher.cpp:1538:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1538 |       prterr(6, "LDKEY is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1539 |                     "Try increasing the size of the workspace.");
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1554:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1554 |             prterr(7, "LDSTP is too small for this problem.\n"
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1555 |                       "Try increasing the size of the workspace.");
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:1596:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 1596 |       prterr(7, "LDSTP is too small for this problem.\n"
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1597 |                     "Try increasing the size of the workspace.");
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘int iwork(int, int*, int, int)’:
fisher.cpp:2001:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 2001 |       prterr(40, "Out of workspace.");
      |                  ^~~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void isort(int*, int*)’:
fisher.cpp:2078:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 2078 |       prterr(20, "This should never occur.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:164:30: 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++)
      |                 ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |       ^~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:206:29: 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:203:15: warning: unused variable ‘totalSNPs’ [-Wunused-variable]
  203 |           int totalSNPs = 0;
      |               ^~~~~~~~~
lookup.cpp:204:15: warning: unused variable ‘gcount’ [-Wunused-variable]
  204 |           int gcount = 0;
      |               ^~~~~~
lookup.cpp:272:31: 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:289:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  289 |           for (int i=25; i<tokens.size()-1; i++)
      |                          ~^~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:332:29: 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:854:28: 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:1332:28: 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:1448:19: warning: unused variable ‘t1’ [-Wunused-variable]
 1448 |               int t1=0;
      |                   ^~
proxy.cpp:169:10: warning: unused variable ‘s’ [-Wunused-variable]
  169 |   CSNP * s = SNP[l];
      |          ^
proxy.cpp:939:65: warning: ‘ref’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  939 |             haplo->HTEST << setw(8) << haplo->rsq_internal(s,ref) << " ";
      |                                                                 ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |           ^~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:83:30: 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:145:30: 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++)
      |                            ~~^~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:396:29: 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:413:36: 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:487:29: 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:802:26: 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:1252:29: 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:1419:35: 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:1477:37: 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++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:683:34: 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:691:34: 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:751:30: 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:791:34: 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:798:34: 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:868:34: 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:872:32: 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:949:29: 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:966:36: 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++)
      |                                  ~~^~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                   ~^~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |              ^~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:137:29: 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:173:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  173 |           if ( tokens.size() <= snp_column ||
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~
clumpld.cpp:174:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  174 |                tokens.size() <= pval_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
clumpld.cpp:201:30: 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:204:26: 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:480:18: 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:520:34: 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:611:34: 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)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:190:27: 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:328:32: 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:358:28: 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++)
      |                          ~~^~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:89:38: 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:97:38: 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:106:34: 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:128:34: 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:132:32: 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:162:38: 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:166:36: 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++)
      |                                   ~^~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:105:26: 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:144:30: 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:161:30: 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:263:31: 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++)
      |                     ~~^~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:239:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  239 |           while (h<nperm)
      |                  ~^~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:402:26: 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:480:16: warning: unused variable ‘a1’ [-Wunused-variable]
  480 |           bool a1 = i2->second;
      |                ^~
profile.cpp:525:16: warning: variable ‘sawNamedAllele’ set but not used [-Wunused-but-set-variable]
  525 |           bool sawNamedAllele = false;
      |                ^~~~~~~~~~~~~~
profile.cpp:629:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<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++)
      |                 ~^~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:239:39: 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 )
      |                 ~~^~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:393:30: 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:1015:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 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:1142:26: 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:1162:30: 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:1231:26: 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:1434:30: 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() )
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:1358:30: warning: unused variable ‘cumU’ [-Wunused-variable]
 1358 |             double cumA = 0, cumU = 0;
      |                              ^~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:298:26: 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:553:24: 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:556:24: 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++)
      |                       ~^~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:247:15: warning: unused variable ‘p1’ [-Wunused-variable]
  247 |           int p1,p2;
      |               ^~
cnv.cpp:247:18: warning: unused variable ‘p2’ [-Wunused-variable]
  247 |           int p1,p2;
      |                  ^~
cnv.cpp:332:19: warning: unused variable ‘p1’ [-Wunused-variable]
  332 |               int p1,p2;
      |                   ^~
cnv.cpp:332:22: warning: unused variable ‘p2’ [-Wunused-variable]
  332 |               int p1,p2;
      |                      ^~
cnv.cpp:678:43: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
  678 |               map<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:825:31: 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:916:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  916 |         if ( par::cnv_freq_include )
      |         ^~
cnv.cpp:922:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  922 |           isection.clear();
      |           ^~~~~~~~
cnv.cpp:1031:32: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable]
 1031 |           set<Range>::iterator i2 = isection.begin();
      |                                ^~
cnv.cpp:1103:43: 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 ];
      |          ^~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:148:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  148 |            tokens.size() <= bp_column )
      |            ~~~~~~~~~~~~~~^~~~~~~~~~~~
greport.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  156 |           if ( tokens.size() <= pval_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
greport.cpp:169:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  169 |           if ( tokens.size() <= snp_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~
greport.cpp:240:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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;
      |       ^~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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;
      |            ^~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:221:34: 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++)
      |                        ~~^~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                     ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:63:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
   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:296:31: 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:502:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:542:38: 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:547:38: 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:553:38: 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:529:24: warning: unused variable ‘seenJoint’ [-Wunused-variable]
  529 |                   bool seenJoint = true;
      |                        ^~~~~~~~~
idhelp.cpp:584:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  584 |                   for (int i = 0 ; i < ids.size() ; i++)
      |                                    ~~^~~~~~~~~~~~
idhelp.cpp:594:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  594 |                   for (int i = 0 ; i < ids.size() ; i++)
      |                                    ~~^~~~~~~~~~~~
idhelp.cpp:678:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:747:30: 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:757:42: 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:836:38: 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:888:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  888 |           if ( tokens.size() != file->uniqFieldCount )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:894:38: 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:903:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  903 |                   if ( j < tokens.size() )
      |                        ~~^~~~~~~~~~~~~~~
idhelp.cpp:922:31: 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:950:35: 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:975:44: 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:1031:21: warning: unused variable ‘v’ [-Wunused-variable]
 1031 |           IDValue & v = *(group->values[j]);
      |                     ^
idhelp.cpp:1070:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1070 |       for ( int g = 0 ; g < idgroup.size(); g++ )
      |                         ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1085:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1085 |           for (int j = 0 ; j < group->values.size(); j++)
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1110:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1110 |           for ( int j = 0; j < group->values.size(); j++ )
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1128:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1128 |               for ( int k = 0; k < (*i0)->values.size(); k++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1183:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1183 |                               for (int z=0; z<group->values.size(); z++)
      |                                             ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1189:46: 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:1245:21: warning: unused variable ‘v’ [-Wunused-variable]
 1245 |           IDValue & v = *(group->values[j]);
      |                     ^
idhelp.cpp:1346:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<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:1649:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 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:1692:26: 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:1710:26: 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:1733:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1733 |               for (int f=0; f<targetFields.size(); f++)
      |                             ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1735:38: 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:1770:30: 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:1784:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 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:1903:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1903 |           for (int i=0; i<fstr.size(); i++)
      |                         ~^~~~~~~~~~~~
idhelp.cpp:1937:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1937 |           for (int k=0; k<h.size(); k++)
      |                         ~^~~~~~~~~
idhelp.cpp:1957:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1957 |           for (int f = 0; f<fieldNames.size(); f++)
      |                           ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:1964:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1964 |               for (int i=0; i<header.size(); i++)
      |                             ~^~~~~~~~~~~~~~
idhelp.cpp:1986:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1986 |           for (int f = 0 ; f < fieldNames.size(); f++)
      |                            ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:2018:29: 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:2024:32: 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:2030:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 2030 |           if ( maxF >= tok.size() )
      |                ~~~~~^~~~~~~~~~~~~
idhelp.cpp:2034:26: 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:2070:34: 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:2168:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 2168 |         for (int j=0; j<headers[k].size(); j++)
      |                       ~^~~~~~~~~~~~~~~~~~
idhelp.cpp:2201:34: 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:2234:30: 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++ )
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                     ~^~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                     ~~^~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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);
      |          ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:110:35: 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:513:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:581:27: 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:601:33: 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:695:29: 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:750:31: 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:989:34: 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:1170:18: warning: unused variable ‘statistic’ [-Wunused-variable]
 1170 |           double statistic = valid ? model->getStatistic() : 0;
      |                  ^~~~~~~~~
dosage.cpp:1252:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1252 |           if ( o->second != dosageFilename_all.size() )
      |                ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
dosage.cpp:1310:21: 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:915:35: warning: ‘snp_code’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  915 |                       SNP[snp_code]->one[personPosition[f][i]] = s1;
      |                                   ^
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:83:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
   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:250:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  250 |           if ( tokens.size() <= chr_column ||
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~
annot.cpp:251:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  251 |                tokens.size() <= bp_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~
annot.cpp:260:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  260 |           if ( tokens.size() <= pval_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
annot.cpp:275:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  275 |           if ( tokens.size() <= snp_column )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~
annot.cpp:300:16: warning: unused variable ‘include’ [-Wunused-variable]
  300 |           bool include = false;
      |                ^~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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:73:35: 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:213:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  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:300:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  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:637:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  637 |             for (int f=0; f<par::meta_files.size(); f++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:680:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
  680 |             for (int f=0; f<par::meta_files.size(); f++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp
In file included from helper.h:24,
                 from r.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: 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:249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |         while (i < nel) {
      |                ~~^~~~~
r.cpp: In member function ‘void Plink::Rfunc()’:
r.cpp:330:15: warning: unused variable ‘ct’ [-Wunused-variable]
  330 |           int ct = data->length();
      |               ^~
r.cpp:380:16: 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;
      |          ^~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp
In file included from Rconnection.cpp:30:
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’:
Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  203 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’:
Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  206 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’:
Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  232 |     char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; }
      |                                          ~^~~~~
Rconnection.h: In member function ‘void Rstrings::decode()’:
Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare]
  245 |       while (i < len) { if (!c[i]) nel++; i++; }
      |              ~~^~~~~
Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |         while (i < nel) {
      |                ~~^~~~~
Rconnection.cpp: At global scope:
Rconnection.cpp:56:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   56 | static char *myID= "Rsrv0103QAP1"; /* this client supports up to protocol version 0103 */
      |                    ^~~~~~~~~~~~~~
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;
      |                           ^~~~
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-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
i686-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck"
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   dh_installdirs -a
   dh_auto_install --destdir=debian/plink/ -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-4_i386.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_i386.deb'.
 dpkg-genbuildinfo --build=any -O../plink_1.07+dfsg-4_i386.buildinfo
 dpkg-genchanges --build=any -O../plink_1.07+dfsg-4_i386.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 2022-04-05T22:08:35Z

Finished
--------

I: Built successfully

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


plink_1.07+dfsg-4_i386.changes:
-------------------------------

Format: 1.8
Date: Sun, 31 Oct 2021 21:01:46 +0530
Source: plink
Binary: plink plink-dbgsym
Built-For-Profiles: cross nocheck
Architecture: i386
Version: 1.07+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
 plink      - whole-genome association analysis toolset
Closes: 984293
Changes:
 plink (1.07+dfsg-4) unstable; urgency=medium
 .
   * Team upload.
   * Add patch to fix FTBFS with gcc-11 (Closes: #984293)
   * Bump Standards-Version to 4.6.0 (no changes needed)
   * Bump debhelper compatibility level to 13
   * Replace ADTTMP with AUTOPKGTEST_TMP
   * Add "Rules-Requires-Root: no"
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 feae437fd97ffe450397bbff938abbb8c408b08160baa1cac5b1e2bab7cd6913 4968 plink_1.07+dfsg-4_i386.buildinfo
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Files:
 3c374268b40e867d9fc5a2e582232563 26533364 debug optional plink-dbgsym_1.07+dfsg-4_i386.deb
 758e7f1d45ffb906c7ff4e43e450c29d 4968 science optional plink_1.07+dfsg-4_i386.buildinfo
 311d69f8e72e53e6e79ab202d1b28ae2 1279280 science optional plink_1.07+dfsg-4_i386.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: plink
Binary: plink plink-dbgsym
Architecture: i386
Version: 1.07+dfsg-4
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Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Tue, 05 Apr 2022 22:08:33 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-6),
 autotools-dev (= 20220109.1),
 base-files (= 12.2),
 base-passwd (= 3.5.52),
 bash (= 5.1-6),
 binutils (= 2.38-3),
 binutils-aarch64-linux-gnu (= 2.38-3),
 binutils-common (= 2.38-3),
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 build-essential (= 12.9),
 bzip2 (= 1.0.8-5),
 coreutils (= 8.32-4.1),
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 dash (= 0.5.11+git20210903+057cd650a4ed-8),
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 debianutils (= 5.7-0.1),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.13.0-1),
 diffutils (= 1:3.7-5),
 dpkg (= 1.21.7),
 dpkg-dev (= 1.21.7),
 dwz (= 0.14-1),
 file (= 1:5.41-3),
 findutils (= 4.9.0-2),
 g++ (= 4:11.2.0-2),
 g++-11 (= 11.2.0-19),
 gcc (= 4:11.2.0-2),
 gcc-11 (= 11.2.0-19),
 gcc-11-base (= 11.2.0-19),
 gcc-12-base (= 12-20220319-1),
 gettext (= 0.21-6),
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 hostname (= 3.23),
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 libblkid1 (= 2.37.3-1+b1),
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 libc-bin (= 2.33-7),
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 libc6-dev (= 2.33-7),
 libcap-ng0 (= 0.7.9-2.2+b2),
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 libcrypt-dev (= 1:4.4.27-1.1),
 libcrypt1 (= 1:4.4.27-1.1),
 libctf-nobfd0 (= 2.38-3),
 libctf0 (= 2.38-3),
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 libgcc-s1 (= 12-20220319-1),
 libgcrypt20 (= 1.10.1-2),
 libgdbm-compat4 (= 1.23-1),
 libgdbm6 (= 1.23-1),
 libgmp10 (= 2:6.2.1+dfsg-3),
 libgomp1 (= 12-20220319-1),
 libgpg-error0 (= 1.43-3),
 libgssapi-krb5-2 (= 1.19.2-2+b1),
 libhwasan0 (= 12-20220319-1),
 libicu67 (= 67.1-7),
 libisl23 (= 0.24-2),
 libitm1 (= 12-20220319-1),
 libk5crypto3 (= 1.19.2-2+b1),
 libkeyutils1 (= 1.6.1-3),
 libkrb5-3 (= 1.19.2-2+b1),
 libkrb5support0 (= 1.19.2-2+b1),
 liblsan0 (= 12-20220319-1),
 liblz4-1 (= 1.9.3-2),
 liblzma5 (= 5.2.5-2),
 libmagic-mgc (= 1:5.41-3),
 libmagic1 (= 1:5.41-3),
 libmount1 (= 2.37.3-1+b1),
 libmpc3 (= 1.2.1-2),
 libmpfr6 (= 4.1.0-3),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libpam-modules (= 1.4.0-11),
 libpam-modules-bin (= 1.4.0-11),
 libpam-runtime (= 1.4.0-11),
 libpam0g (= 1.4.0-11),
 libpcre2-8-0 (= 10.39-3),
 libpcre3 (= 2:8.39-14),
 libperl5.34 (= 5.34.0-3),
 libpipeline1 (= 1.5.5-1),
 libseccomp2 (= 2.5.3-2),
 libselinux1 (= 3.3-1+b2),
 libsigsegv2 (= 2.14-1),
 libsmartcols1 (= 2.37.3-1+b1),
 libssl1.1 (= 1.1.1n-1),
 libstdc++-11-dev (= 11.2.0-19),
 libstdc++6 (= 12-20220319-1),
 libsub-override-perl (= 0.09-2),
 libsystemd0 (= 250.4-1),
 libtinfo6 (= 6.3-2),
 libtirpc-common (= 1.3.2-2),
 libtirpc-dev (= 1.3.2-2),
 libtirpc3 (= 1.3.2-2),
 libtool (= 2.4.7-2),
 libtsan0 (= 11.2.0-19),
 libubsan1 (= 12-20220319-1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 250.4-1),
 libunistring2 (= 1.0-1),
 libuuid1 (= 2.37.3-1+b1),
 libxml2 (= 2.9.13+dfsg-1),
 libzstd1 (= 1.4.10+dfsg-1),
 linux-libc-dev (= 5.16.18-1),
 login (= 1:4.11.1+dfsg1-2),
 lsb-base (= 11.1.0),
 m4 (= 1.4.18-5),
 make (= 4.3-4.1),
 man-db (= 2.10.2-1),
 mawk (= 1.3.4.20200120-3),
 ncurses-base (= 6.3-2),
 ncurses-bin (= 6.3-2),
 patch (= 2.7.6-7),
 perl (= 5.34.0-3),
 perl-base (= 5.34.0-3),
 perl-modules-5.34 (= 5.34.0-3),
 po-debconf (= 1.0.21+nmu1),
 rpcsvc-proto (= 1.4.2-4),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sysvinit-utils (= 3.01-1),
 tar (= 1.34+dfsg-1),
 util-linux (= 2.37.3-1+b1),
 xz-utils (= 5.2.5-2),
 zlib1g (= 1:1.2.11.dfsg-4),
 zlib1g-dev (= 1:1.2.11.dfsg-4)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1635694306"


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


plink-dbgsym_1.07+dfsg-4_i386.deb
---------------------------------

 new Debian package, version 2.0.
 size 26533364 bytes: control archive=536 bytes.
     371 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: plink-dbgsym
 Source: plink
 Version: 1.07+dfsg-4
 Auto-Built-Package: debug-symbols
 Architecture: i386
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 26302
 Depends: plink (= 1.07+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for plink
 Build-Ids: 3c17176e7d8ef9533a4e9310aadc925800b9ac1f

drwxr-xr-x root/root         0 2021-10-31 15:31 ./
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debug/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debug/.build-id/3c/
-rw-r--r-- root/root  26922736 2021-10-31 15:31 ./usr/lib/debug/.build-id/3c/17176e7d8ef9533a4e9310aadc925800b9ac1f.debug
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/share/doc/plink-dbgsym -> plink


plink_1.07+dfsg-4_i386.deb
--------------------------

 new Debian package, version 2.0.
 size 1279280 bytes: control archive=1296 bytes.
    1093 bytes,    26 lines      control              
     915 bytes,    13 lines      md5sums              
 Package: plink
 Version: 1.07+dfsg-4
 Architecture: i386
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4076
 Depends: libc6 (>= 2.29), libcrypt1 (>= 1:4.1.0), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), 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 2021-10-31 15:31 ./
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/bin/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/bin/p-link -> ../lib/debian-med/bin/plink
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/bin/plink1 -> ../lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/bin/
-rwxr-xr-x root/root   4124384 2021-10-31 15:31 ./usr/lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/plink.1.gz -> ../../../../../share/man/man1/p-link.1.gz
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/plink/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/plink/plink -> ../debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/
-rw-r--r-- root/root       566 2021-10-31 15:11 ./usr/share/doc/plink/NEWS.Debian.gz
-rw-r--r-- root/root      1894 2021-10-31 15:11 ./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      2505 2021-10-31 15:31 ./usr/share/doc/plink/changelog.Debian.gz
-rw-r--r-- root/root      8639 2021-10-31 15:11 ./usr/share/doc/plink/changelog.gz
-rw-r--r-- root/root      2290 2021-10-31 15:11 ./usr/share/doc/plink/copyright
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/examples/
-rw-r--r-- root/root       358 2021-10-31 15:11 ./usr/share/doc/plink/examples/README
-rw-r--r-- root/root       267 2021-10-31 15:11 ./usr/share/doc/plink/examples/expected.plink.assoc
-rw-r--r-- root/root       126 2021-10-31 15:11 ./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 2021-10-31 15:31 ./usr/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/man/man1/
-rw-r--r-- root/root       688 2021-10-31 15:31 ./usr/share/man/man1/p-link.1.gz
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/share/man/man1/plink1.1.gz -> p-link.1.gz


lintian
-------


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

Merged Build-Depends: lintian:arm64
Filtered Build-Depends: lintian:arm64
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 [541 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [625 B]
Fetched 2129 B in 0s (47.8 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 libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl
  libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl
  liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl
  libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
  libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
  libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl
  libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzip lzop patchutils readline-common t1utils
  unzip
Suggested packages:
  libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl
  libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libwww-perl
  binutils-multiarch libtext-template-perl readline-doc zip
Recommended packages:
  gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl
  libpackage-stash-xs-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl
  libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl
  liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl
  libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
  libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
  libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl
  libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzip lzop patchutils readline-common
  sbuild-build-depends-lintian-dummy:i386 t1utils unzip
0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded.
Need to get 7644 kB of archives.
After this operation, 22.9 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://mirror.einval.org/debian sid/main arm64 readline-common all 8.1.2-1 [73.8 kB]
Get:3 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1.2-1 [160 kB]
Get:4 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB]
Get:5 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-1 [49.3 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-3+b1 [540 kB]
Get:7 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.38.2-1 [779 kB]
Get:8 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-3+b1 [884 kB]
Get:9 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB]
Get:10 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40+b1 [69.2 kB]
Get:11 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b4 [11.2 kB]
Get:12 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB]
Get:13 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b3 [15.8 kB]
Get:14 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b4 [25.5 kB]
Get:15 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:16 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.31-1 [24.2 kB]
Get:17 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB]
Get:18 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:19 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-1+b4 [44.2 kB]
Get:20 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:21 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:22 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:23 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB]
Get:24 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-3+b8 [36.4 kB]
Get:25 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b2 [15.3 kB]
Get:26 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.28-1 [17.3 kB]
Get:27 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b2 [25.2 kB]
Get:28 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB]
Get:29 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB]
Get:30 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB]
Get:31 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-1.1 [8552 B]
Get:32 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.27-1+b1 [127 kB]
Get:33 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:34 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:35 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB]
Get:36 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB]
Get:37 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB]
Get:38 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2+b1 [36.9 kB]
Get:39 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB]
Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB]
Get:41 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1 [34.6 kB]
Get:42 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB]
Get:43 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB]
Get:44 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:45 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0001-1 [32.2 kB]
Get:46 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-1+b6 [103 kB]
Get:47 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB]
Get:48 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB]
Get:49 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b3 [25.8 kB]
Get:50 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b4 [26.7 kB]
Get:51 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB]
Get:52 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB]
Get:53 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B]
Get:54 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B]
Get:55 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB]
Get:56 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB]
Get:57 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB]
Get:58 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB]
Get:59 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB]
Get:60 http://mirror.einval.org/debian sid/main arm64 libio-prompt-tiny-perl all 0.003-1 [9150 B]
Get:61 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB]
Get:62 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB]
Get:63 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB]
Get:64 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB]
Get:65 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB]
Get:66 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB]
Get:67 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB]
Get:68 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:69 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB]
Get:70 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB]
Get:71 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:72 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB]
Get:73 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b2 [171 kB]
Get:74 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:75 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b4 [11.9 kB]
Get:76 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b2 [13.5 kB]
Get:77 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:78 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.122-1 [56.0 kB]
Get:79 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b8 [17.0 kB]
Get:80 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.009-1+b1 [11.9 kB]
Get:81 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1+b1 [46.4 kB]
Get:82 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.023+ds-1 [95.0 kB]
Get:83 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.023+ds-1 [97.9 kB]
Get:84 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-1 [11.0 kB]
Get:85 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.22-1 [50.3 kB]
Get:86 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.27-1 [28.2 kB]
Get:87 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-1+b3 [27.2 kB]
Get:88 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b9 [8660 B]
Get:89 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1+b1 [13.4 kB]
Get:90 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1+b1 [194 kB]
Get:91 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB]
Get:92 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b4 [74.7 kB]
Get:93 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:94 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b3 [19.8 kB]
Get:95 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.10-1 [91.0 kB]
Get:96 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB]
Get:97 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1+b1 [34.4 kB]
Get:98 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.23-3 [86.6 kB]
Get:99 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB]
Get:100 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB]
Get:101 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB]
Get:102 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB]
Get:103 http://mirror.einval.org/debian sid/main arm64 lintian all 2.114.0 [1382 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libcpanel-json-xs-perl:arm64.
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Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.114.0) ...
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I: Lintian run was successful.

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| Post Build                                                                   |
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| Cleanup                                                                      |
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+------------------------------------------------------------------------------+
| Summary                                                                      |
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Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 313872
Build-Time: 1772
Distribution: unstable
Foreign Architectures: i386
Host Architecture: i386
Install-Time: 35
Job: plink_1.07+dfsg-4
Lintian: pass
Machine Architecture: arm64
Package: plink
Package-Time: 1837
Source-Version: 1.07+dfsg-4
Space: 313872
Status: successful
Version: 1.07+dfsg-4
--------------------------------------------------------------------------------
Finished at 2022-04-05T22:08:35Z
Build needed 00:30:37, 313872k disk space