sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley

+==============================================================================+
| plink 1.07+dfsg-4 (mips64el)                 Mon, 17 Apr 2023 01:25:08 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-4
Source Version: 1.07+dfsg-4
Distribution: unstable
Machine Architecture: amd64
Host Architecture: mips64el
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-70b1fdf0-e8ee-46d8-aec3-ad9723cc7c32' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-VUruUi/resolver-MM7UhI' with '<<RESOLVERDIR>>'

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

Hit:1 http://localhost:3142/debian sid InRelease
Get:2 http://localhost:3142/debian sid/main mips64el Packages [9065 kB]
Fetched 9065 kB in 1s (7744 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://localhost:3142/debian sid/main plink 1.07+dfsg-4 (dsc) [2076 B]
Get:2 http://localhost:3142/debian sid/main plink 1.07+dfsg-4 (tar) [429 kB]
Get:3 http://localhost:3142/debian sid/main plink 1.07+dfsg-4 (diff) [17.4 kB]
Fetched 449 kB in 0s (8156 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-VUruUi/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-VUruUi' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64, libc-dev:mips64el, libstdc++-dev:mips64el
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64, libc-dev:mips64el, libstdc++-dev:mips64el
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [410 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [502 B]
Fetched 1869 B in 0s (0 B/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-mips64el-linux-gnuabi64
  bsdextrautils cpp-12-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64
  cross-config crossbuild-essential-mips64el debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++-12-mips64el-linux-gnuabi64
  g++-mips64el-linux-gnuabi64 gcc-11-base:mips64el gcc-12-base:mips64el
  gcc-12-cross-base-mipsen gcc-12-mips64el-linux-gnuabi64
  gcc-12-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl
  libatomic1:mips64el libatomic1-mips64el-cross libc6:mips64el
  libc6-dev:mips64el libc6-dev-mips64el-cross libc6-mips64el-cross
  libcom-err2:mips64el libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:mips64el libcrypt1:mips64el libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:mips64el
  libgcc-12-dev-mips64el-cross libgcc-s1:mips64el libgcc-s1-mips64el-cross
  libgomp1:mips64el libgomp1-mips64el-cross libgssapi-krb5-2:mips64el libicu72
  libio-string-perl libk5crypto3:mips64el libkeyutils1:mips64el
  libkrb5-3:mips64el libkrb5support0:mips64el liblocale-gettext-perl
  libmagic-mgc libmagic1 libnsl-dev:mips64el libnsl2:mips64el libpipeline1
  libssl3:mips64el libstdc++-11-dev:mips64el libstdc++-12-dev-mips64el-cross
  libstdc++6:mips64el libstdc++6-mips64el-cross libsub-override-perl
  libtirpc-dev:mips64el libtirpc3:mips64el libtool libuchardet0
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:mips64el linux-libc-dev-mips64el-cross m4 man-db po-debconf
  sensible-utils ucf zlib1g:mips64el zlib1g-dev:mips64el
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales
  cpp-12-doc cpp-doc dh-make binutils-multiarch
  g++-12-multilib-mips64el-linux-gnuabi64 gcc-12-doc
  gcc-12-multilib-mips64el-linux-gnuabi64 manpages-dev flex bison
  gdb-mips64el-linux-gnuabi64 gcc-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff glibc-doc:mips64el libc-l10n:mips64el
  locales:mips64el libnss-nis:mips64el libnss-nisplus:mips64el
  manpages-dev:mips64el krb5-doc:mips64el krb5-user:mips64el
  libstdc++-11-doc:mips64el 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:mips64el libarchive-cpio-perl
  krb5-locales:mips64el 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-mips64el-linux-gnuabi64
  bsdextrautils cpp-12-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64
  cross-config crossbuild-essential-mips64el debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dwz file g++-12-mips64el-linux-gnuabi64
  g++-mips64el-linux-gnuabi64 gcc-11-base:mips64el gcc-12-base:mips64el
  gcc-12-cross-base-mipsen gcc-12-mips64el-linux-gnuabi64
  gcc-12-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl
  libatomic1:mips64el libatomic1-mips64el-cross libc6:mips64el
  libc6-dev:mips64el libc6-dev-mips64el-cross libc6-mips64el-cross
  libcom-err2:mips64el libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:mips64el libcrypt1:mips64el libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:mips64el
  libgcc-12-dev-mips64el-cross libgcc-s1:mips64el libgcc-s1-mips64el-cross
  libgomp1:mips64el libgomp1-mips64el-cross libgssapi-krb5-2:mips64el libicu72
  libio-string-perl libk5crypto3:mips64el libkeyutils1:mips64el
  libkrb5-3:mips64el libkrb5support0:mips64el liblocale-gettext-perl
  libmagic-mgc libmagic1 libnsl-dev:mips64el libnsl2:mips64el libpipeline1
  libssl3:mips64el libstdc++-11-dev:mips64el libstdc++-12-dev-mips64el-cross
  libstdc++6:mips64el libstdc++6-mips64el-cross libsub-override-perl
  libtirpc-dev:mips64el libtirpc3:mips64el libtool libuchardet0
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:mips64el linux-libc-dev-mips64el-cross m4 man-db po-debconf
  sbuild-build-depends-main-dummy:mips64el sensible-utils ucf zlib1g:mips64el
  zlib1g-dev:mips64el
0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded.
Need to get 75.4 MB of archives.
After this operation, 314 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B]
Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB]
Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB]
Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-12 [495 kB]
Get:19 http://localhost:3142/debian sid/main amd64 binutils-mips64el-linux-gnuabi64 amd64 2.40-2cross2 [2798 kB]
Get:20 http://localhost:3142/debian sid/main amd64 gcc-12-mips64el-linux-gnuabi64-base amd64 12.2.0-14cross5 [37.7 kB]
Get:21 http://localhost:3142/debian sid/main amd64 cpp-12-mips64el-linux-gnuabi64 amd64 12.2.0-14cross5 [8093 kB]
Get:22 http://localhost:3142/debian sid/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:12.2.0-4 [3296 B]
Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB]
Get:24 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base-mipsen all 12.2.0-14cross5 [33.3 kB]
Get:25 http://localhost:3142/debian sid/main amd64 libc6-mips64el-cross all 2.36-8cross2 [1057 kB]
Get:26 http://localhost:3142/debian sid/main amd64 libgcc-s1-mips64el-cross all 12.2.0-14cross5 [70.9 kB]
Get:27 http://localhost:3142/debian sid/main amd64 libgomp1-mips64el-cross all 12.2.0-14cross5 [102 kB]
Get:28 http://localhost:3142/debian sid/main amd64 libatomic1-mips64el-cross all 12.2.0-14cross5 [7172 B]
Get:29 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-mips64el-cross all 12.2.0-14cross5 [294 kB]
Get:30 http://localhost:3142/debian sid/main amd64 gcc-12-mips64el-linux-gnuabi64 amd64 12.2.0-14cross5 [15.9 MB]
Get:31 http://localhost:3142/debian sid/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:12.2.0-4 [1480 B]
Get:32 http://localhost:3142/debian sid/main amd64 libstdc++6-mips64el-cross all 12.2.0-14cross5 [504 kB]
Get:33 http://localhost:3142/debian sid/main amd64 linux-libc-dev-mips64el-cross all 6.1.8-1cross2 [1837 kB]
Get:34 http://localhost:3142/debian sid/main amd64 libc6-dev-mips64el-cross all 2.36-8cross2 [1572 kB]
Get:35 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-mips64el-cross all 12.2.0-14cross5 [2065 kB]
Get:36 http://localhost:3142/debian sid/main amd64 g++-12-mips64el-linux-gnuabi64 amd64 12.2.0-14cross5 [9008 kB]
Get:37 http://localhost:3142/debian sid/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:12.2.0-4 [1188 B]
Get:38 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB]
Get:39 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:40 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get:41 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get:42 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:43 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:44 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:45 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB]
Get:46 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:47 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB]
Get:48 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB]
Get:49 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get:50 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get:51 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB]
Get:52 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB]
Get:53 http://localhost:3142/debian sid/main amd64 crossbuild-essential-mips64el all 12.9 [6740 B]
Get:54 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get:55 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB]
Get:56 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:57 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:58 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get:59 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:60 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:61 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get:62 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB]
Get:63 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-12 [1300 kB]
Get:64 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:65 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:66 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.4 [942 kB]
Get:67 http://localhost:3142/debian sid/main mips64el gcc-11-base mips64el 11.3.0-12 [38.4 kB]
Get:68 http://localhost:3142/debian sid/main mips64el gcc-12-base mips64el 12.2.0-14 [37.5 kB]
Get:69 http://localhost:3142/debian sid/main mips64el libgcc-s1 mips64el 12.2.0-14 [70.5 kB]
Get:70 http://localhost:3142/debian sid/main mips64el libc6 mips64el 2.36-9 [2376 kB]
Get:71 http://localhost:3142/debian sid/main mips64el libatomic1 mips64el 12.2.0-14 [7444 B]
Get:72 http://localhost:3142/debian sid/main mips64el linux-libc-dev mips64el 6.1.20-2 [1745 kB]
Get:73 http://localhost:3142/debian sid/main mips64el libcrypt1 mips64el 1:4.4.33-2 [94.0 kB]
Get:74 http://localhost:3142/debian sid/main mips64el libcrypt-dev mips64el 1:4.4.33-2 [127 kB]
Get:75 http://localhost:3142/debian sid/main mips64el libcom-err2 mips64el 1.47.0-2 [19.6 kB]
Get:76 http://localhost:3142/debian sid/main mips64el libkrb5support0 mips64el 1.20.1-1+b1 [30.4 kB]
Get:77 http://localhost:3142/debian sid/main mips64el libk5crypto3 mips64el 1.20.1-1+b1 [85.5 kB]
Get:78 http://localhost:3142/debian sid/main mips64el libkeyutils1 mips64el 1.6.3-2 [8432 B]
Get:79 http://localhost:3142/debian sid/main mips64el libssl3 mips64el 3.0.8-1 [1486 kB]
Get:80 http://localhost:3142/debian sid/main mips64el libkrb5-3 mips64el 1.20.1-1+b1 [296 kB]
Get:81 http://localhost:3142/debian sid/main mips64el libgssapi-krb5-2 mips64el 1.20.1-1+b1 [117 kB]
Get:82 http://localhost:3142/debian sid/main mips64el libtirpc3 mips64el 1.3.3+ds-1 [74.9 kB]
Get:83 http://localhost:3142/debian sid/main mips64el libnsl2 mips64el 1.3.0-2 [35.5 kB]
Get:84 http://localhost:3142/debian sid/main mips64el libtirpc-dev mips64el 1.3.3+ds-1 [200 kB]
Get:85 http://localhost:3142/debian sid/main mips64el libnsl-dev mips64el 1.3.0-2 [70.3 kB]
Get:86 http://localhost:3142/debian sid/main mips64el libc6-dev mips64el 2.36-9 [1576 kB]
Get:87 http://localhost:3142/debian sid/main mips64el libgomp1 mips64el 12.2.0-14 [104 kB]
Get:88 http://localhost:3142/debian sid/main mips64el libgcc-11-dev mips64el 11.3.0-12 [281 kB]
Get:89 http://localhost:3142/debian sid/main mips64el libstdc++6 mips64el 12.2.0-14 [546 kB]
Get:90 http://localhost:3142/debian sid/main mips64el libstdc++-11-dev mips64el 11.3.0-12 [2004 kB]
Get:91 http://localhost:3142/debian sid/main mips64el zlib1g mips64el 1:1.2.13.dfsg-1 [77.9 kB]
Get:92 http://localhost:3142/debian sid/main mips64el zlib1g-dev mips64el 1:1.2.13.dfsg-1 [909 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 75.4 MB in 0s (177 MB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 15279 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package ucf.
Preparing to unpack .../11-ucf_3.0043+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043+nmu1) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package binutils-mips64el-linux-gnuabi64.
Preparing to unpack .../17-binutils-mips64el-linux-gnuabi64_2.40-2cross2_amd64.deb ...
Unpacking binutils-mips64el-linux-gnuabi64 (2.40-2cross2) ...
Selecting previously unselected package gcc-12-mips64el-linux-gnuabi64-base:amd64.
Preparing to unpack .../18-gcc-12-mips64el-linux-gnuabi64-base_12.2.0-14cross5_amd64.deb ...
Unpacking gcc-12-mips64el-linux-gnuabi64-base:amd64 (12.2.0-14cross5) ...
Selecting previously unselected package cpp-12-mips64el-linux-gnuabi64.
Preparing to unpack .../19-cpp-12-mips64el-linux-gnuabi64_12.2.0-14cross5_amd64.deb ...
Unpacking cpp-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Selecting previously unselected package cpp-mips64el-linux-gnuabi64.
Preparing to unpack .../20-cpp-mips64el-linux-gnuabi64_4%3a12.2.0-4_amd64.deb ...
Unpacking cpp-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Selecting previously unselected package cross-config.
Preparing to unpack .../21-cross-config_2.6.20_all.deb ...
Unpacking cross-config (2.6.20) ...
Selecting previously unselected package gcc-12-cross-base-mipsen.
Preparing to unpack .../22-gcc-12-cross-base-mipsen_12.2.0-14cross5_all.deb ...
Unpacking gcc-12-cross-base-mipsen (12.2.0-14cross5) ...
Selecting previously unselected package libc6-mips64el-cross.
Preparing to unpack .../23-libc6-mips64el-cross_2.36-8cross2_all.deb ...
Unpacking libc6-mips64el-cross (2.36-8cross2) ...
Selecting previously unselected package libgcc-s1-mips64el-cross.
Preparing to unpack .../24-libgcc-s1-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libgcc-s1-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package libgomp1-mips64el-cross.
Preparing to unpack .../25-libgomp1-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libgomp1-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package libatomic1-mips64el-cross.
Preparing to unpack .../26-libatomic1-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libatomic1-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package libgcc-12-dev-mips64el-cross.
Preparing to unpack .../27-libgcc-12-dev-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libgcc-12-dev-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package gcc-12-mips64el-linux-gnuabi64.
Preparing to unpack .../28-gcc-12-mips64el-linux-gnuabi64_12.2.0-14cross5_amd64.deb ...
Unpacking gcc-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Selecting previously unselected package gcc-mips64el-linux-gnuabi64.
Preparing to unpack .../29-gcc-mips64el-linux-gnuabi64_4%3a12.2.0-4_amd64.deb ...
Unpacking gcc-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Selecting previously unselected package libstdc++6-mips64el-cross.
Preparing to unpack .../30-libstdc++6-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libstdc++6-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package linux-libc-dev-mips64el-cross.
Preparing to unpack .../31-linux-libc-dev-mips64el-cross_6.1.8-1cross2_all.deb ...
Unpacking linux-libc-dev-mips64el-cross (6.1.8-1cross2) ...
Selecting previously unselected package libc6-dev-mips64el-cross.
Preparing to unpack .../32-libc6-dev-mips64el-cross_2.36-8cross2_all.deb ...
Unpacking libc6-dev-mips64el-cross (2.36-8cross2) ...
Selecting previously unselected package libstdc++-12-dev-mips64el-cross.
Preparing to unpack .../33-libstdc++-12-dev-mips64el-cross_12.2.0-14cross5_all.deb ...
Unpacking libstdc++-12-dev-mips64el-cross (12.2.0-14cross5) ...
Selecting previously unselected package g++-12-mips64el-linux-gnuabi64.
Preparing to unpack .../34-g++-12-mips64el-linux-gnuabi64_12.2.0-14cross5_amd64.deb ...
Unpacking g++-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Selecting previously unselected package g++-mips64el-linux-gnuabi64.
Preparing to unpack .../35-g++-mips64el-linux-gnuabi64_4%3a12.2.0-4_amd64.deb ...
Unpacking g++-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Selecting previously unselected package libconfig-inifiles-perl.
Preparing to unpack .../36-libconfig-inifiles-perl_3.000003-2_all.deb ...
Unpacking libconfig-inifiles-perl (3.000003-2) ...
Selecting previously unselected package libio-string-perl.
Preparing to unpack .../37-libio-string-perl_1.08-4_all.deb ...
Unpacking libio-string-perl (1.08-4) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../38-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../39-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package libxml-namespacesupport-perl.
Preparing to unpack .../40-libxml-namespacesupport-perl_1.12-2_all.deb ...
Unpacking libxml-namespacesupport-perl (1.12-2) ...
Selecting previously unselected package libxml-sax-base-perl.
Preparing to unpack .../41-libxml-sax-base-perl_1.09-3_all.deb ...
Unpacking libxml-sax-base-perl (1.09-3) ...
Selecting previously unselected package libxml-sax-perl.
Preparing to unpack .../42-libxml-sax-perl_1.02+dfsg-3_all.deb ...
Unpacking libxml-sax-perl (1.02+dfsg-3) ...
Selecting previously unselected package libxml-libxml-perl.
Preparing to unpack .../43-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1_amd64.deb ...
Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ...
Selecting previously unselected package libxml-simple-perl.
Preparing to unpack .../44-libxml-simple-perl_2.25-2_all.deb ...
Unpacking libxml-simple-perl (2.25-2) ...
Selecting previously unselected package libyaml-perl.
Preparing to unpack .../45-libyaml-perl_1.30-2_all.deb ...
Unpacking libyaml-perl (1.30-2) ...
Selecting previously unselected package libconfig-auto-perl.
Preparing to unpack .../46-libconfig-auto-perl_0.44-2_all.deb ...
Unpacking libconfig-auto-perl (0.44-2) ...
Selecting previously unselected package libfile-which-perl.
Preparing to unpack .../47-libfile-which-perl_1.27-2_all.deb ...
Unpacking libfile-which-perl (1.27-2) ...
Selecting previously unselected package libfile-homedir-perl.
Preparing to unpack .../48-libfile-homedir-perl_1.006-2_all.deb ...
Unpacking libfile-homedir-perl (1.006-2) ...
Selecting previously unselected package libdebian-dpkgcross-perl.
Preparing to unpack .../49-libdebian-dpkgcross-perl_2.6.20_all.deb ...
Unpacking libdebian-dpkgcross-perl (2.6.20) ...
Selecting previously unselected package dpkg-cross.
Preparing to unpack .../50-dpkg-cross_2.6.20_all.deb ...
Unpacking dpkg-cross (2.6.20) ...
Selecting previously unselected package crossbuild-essential-mips64el.
Preparing to unpack .../51-crossbuild-essential-mips64el_12.9_all.deb ...
Unpacking crossbuild-essential-mips64el (12.9) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../52-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../53-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../54-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../55-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../56-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../57-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../58-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../59-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../60-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../61-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../62-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../63-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../64-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package gcc-11-base:mips64el.
Preparing to unpack .../65-gcc-11-base_11.3.0-12_mips64el.deb ...
Unpacking gcc-11-base:mips64el (11.3.0-12) ...
Selecting previously unselected package gcc-12-base:mips64el.
Preparing to unpack .../66-gcc-12-base_12.2.0-14_mips64el.deb ...
Unpacking gcc-12-base:mips64el (12.2.0-14) ...
Selecting previously unselected package libgcc-s1:mips64el.
Preparing to unpack .../67-libgcc-s1_12.2.0-14_mips64el.deb ...
Unpacking libgcc-s1:mips64el (12.2.0-14) ...
Selecting previously unselected package libc6:mips64el.
Preparing to unpack .../68-libc6_2.36-9_mips64el.deb ...
Unpacking libc6:mips64el (2.36-9) ...
Selecting previously unselected package libatomic1:mips64el.
Preparing to unpack .../69-libatomic1_12.2.0-14_mips64el.deb ...
Unpacking libatomic1:mips64el (12.2.0-14) ...
Selecting previously unselected package linux-libc-dev:mips64el.
Preparing to unpack .../70-linux-libc-dev_6.1.20-2_mips64el.deb ...
Unpacking linux-libc-dev:mips64el (6.1.20-2) ...
Selecting previously unselected package libcrypt1:mips64el.
Preparing to unpack .../71-libcrypt1_1%3a4.4.33-2_mips64el.deb ...
Unpacking libcrypt1:mips64el (1:4.4.33-2) ...
Selecting previously unselected package libcrypt-dev:mips64el.
Preparing to unpack .../72-libcrypt-dev_1%3a4.4.33-2_mips64el.deb ...
Unpacking libcrypt-dev:mips64el (1:4.4.33-2) ...
Selecting previously unselected package libcom-err2:mips64el.
Preparing to unpack .../73-libcom-err2_1.47.0-2_mips64el.deb ...
Unpacking libcom-err2:mips64el (1.47.0-2) ...
Selecting previously unselected package libkrb5support0:mips64el.
Preparing to unpack .../74-libkrb5support0_1.20.1-1+b1_mips64el.deb ...
Unpacking libkrb5support0:mips64el (1.20.1-1+b1) ...
Selecting previously unselected package libk5crypto3:mips64el.
Preparing to unpack .../75-libk5crypto3_1.20.1-1+b1_mips64el.deb ...
Unpacking libk5crypto3:mips64el (1.20.1-1+b1) ...
Selecting previously unselected package libkeyutils1:mips64el.
Preparing to unpack .../76-libkeyutils1_1.6.3-2_mips64el.deb ...
Unpacking libkeyutils1:mips64el (1.6.3-2) ...
Selecting previously unselected package libssl3:mips64el.
Preparing to unpack .../77-libssl3_3.0.8-1_mips64el.deb ...
Unpacking libssl3:mips64el (3.0.8-1) ...
Selecting previously unselected package libkrb5-3:mips64el.
Preparing to unpack .../78-libkrb5-3_1.20.1-1+b1_mips64el.deb ...
Unpacking libkrb5-3:mips64el (1.20.1-1+b1) ...
Selecting previously unselected package libgssapi-krb5-2:mips64el.
Preparing to unpack .../79-libgssapi-krb5-2_1.20.1-1+b1_mips64el.deb ...
Unpacking libgssapi-krb5-2:mips64el (1.20.1-1+b1) ...
Selecting previously unselected package libtirpc3:mips64el.
Preparing to unpack .../80-libtirpc3_1.3.3+ds-1_mips64el.deb ...
Unpacking libtirpc3:mips64el (1.3.3+ds-1) ...
Selecting previously unselected package libnsl2:mips64el.
Preparing to unpack .../81-libnsl2_1.3.0-2_mips64el.deb ...
Unpacking libnsl2:mips64el (1.3.0-2) ...
Selecting previously unselected package libtirpc-dev:mips64el.
Preparing to unpack .../82-libtirpc-dev_1.3.3+ds-1_mips64el.deb ...
Unpacking libtirpc-dev:mips64el (1.3.3+ds-1) ...
Selecting previously unselected package libnsl-dev:mips64el.
Preparing to unpack .../83-libnsl-dev_1.3.0-2_mips64el.deb ...
Unpacking libnsl-dev:mips64el (1.3.0-2) ...
Selecting previously unselected package libc6-dev:mips64el.
Preparing to unpack .../84-libc6-dev_2.36-9_mips64el.deb ...
Unpacking libc6-dev:mips64el (2.36-9) ...
Selecting previously unselected package libgomp1:mips64el.
Preparing to unpack .../85-libgomp1_12.2.0-14_mips64el.deb ...
Unpacking libgomp1:mips64el (12.2.0-14) ...
Selecting previously unselected package libgcc-11-dev:mips64el.
Preparing to unpack .../86-libgcc-11-dev_11.3.0-12_mips64el.deb ...
Unpacking libgcc-11-dev:mips64el (11.3.0-12) ...
Selecting previously unselected package libstdc++6:mips64el.
Preparing to unpack .../87-libstdc++6_12.2.0-14_mips64el.deb ...
Unpacking libstdc++6:mips64el (12.2.0-14) ...
Selecting previously unselected package libstdc++-11-dev:mips64el.
Preparing to unpack .../88-libstdc++-11-dev_11.3.0-12_mips64el.deb ...
Unpacking libstdc++-11-dev:mips64el (11.3.0-12) ...
Selecting previously unselected package zlib1g:mips64el.
Preparing to unpack .../89-zlib1g_1%3a1.2.13.dfsg-1_mips64el.deb ...
Unpacking zlib1g:mips64el (1:1.2.13.dfsg-1) ...
Selecting previously unselected package zlib1g-dev:mips64el.
Preparing to unpack .../90-zlib1g-dev_1%3a1.2.13.dfsg-1_mips64el.deb ...
Unpacking zlib1g-dev:mips64el (1:1.2.13.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy:mips64el.
Preparing to unpack .../91-sbuild-build-depends-main-dummy_0.invalid.0_mips64el.deb ...
Unpacking sbuild-build-depends-main-dummy:mips64el (0.invalid.0) ...
Setting up libconfig-inifiles-perl (3.000003-2) ...
Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up gcc-11-base:mips64el (11.3.0-12) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:amd64 (1:5.44-3) ...
Setting up gcc-12-cross-base-mipsen (12.2.0-14cross5) ...
Setting up linux-libc-dev:mips64el (6.1.20-2) ...
Setting up libc6-mips64el-cross (2.36-8cross2) ...
Setting up libxml-namespacesupport-perl (1.12-2) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up libyaml-perl (1.30-2) ...
Setting up binutils-mips64el-linux-gnuabi64 (2.40-2cross2) ...
Setting up gcc-12-base:mips64el (12.2.0-14) ...
Setting up libxml-sax-base-perl (1.09-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up cross-config (2.6.20) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up linux-libc-dev-mips64el-cross (6.1.8-1cross2) ...
Setting up gcc-12-mips64el-linux-gnuabi64-base:amd64 (12.2.0-14cross5) ...
Setting up cpp-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up cpp-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Setting up libgomp1-mips64el-cross (12.2.0-14cross5) ...
Setting up libgcc-s1-mips64el-cross (12.2.0-14cross5) ...
Setting up libelf1:amd64 (0.188-2.1) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ...
Setting up liblocale-gettext-perl (1.07-5) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libatomic1-mips64el-cross (12.2.0-14cross5) ...
Setting up libtool (2.4.7-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libc6-dev-mips64el-cross (2.36-8cross2) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libstdc++6-mips64el-cross (12.2.0-14cross5) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up libgcc-12-dev-mips64el-cross (12.2.0-14cross5) ...
Setting up gcc-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Setting up libstdc++-12-dev-mips64el-cross (12.2.0-14cross5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up g++-12-mips64el-linux-gnuabi64 (12.2.0-14cross5) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+dfsg-3) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up gcc-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up g++-mips64el-linux-gnuabi64 (4:12.2.0-4) ...
Setting up debhelper (13.11.4) ...
Setting up libxml-simple-perl (2.25-2) ...
Setting up libconfig-auto-perl (0.44-2) ...
Setting up libdebian-dpkgcross-perl (2.6.20) ...
Setting up dpkg-cross (2.6.20) ...
Setting up crossbuild-essential-mips64el (12.9) ...
Setting up libgcc-s1:mips64el (12.2.0-14) ...
Setting up libc6:mips64el (2.36-9) ...
Setting up libstdc++6:mips64el (12.2.0-14) ...
Setting up libkeyutils1:mips64el (1.6.3-2) ...
Setting up libssl3:mips64el (3.0.8-1) ...
Setting up zlib1g:mips64el (1:1.2.13.dfsg-1) ...
Setting up libcrypt1:mips64el (1:4.4.33-2) ...
Setting up libcom-err2:mips64el (1.47.0-2) ...
Setting up libgomp1:mips64el (12.2.0-14) ...
Setting up libkrb5support0:mips64el (1.20.1-1+b1) ...
Setting up libatomic1:mips64el (12.2.0-14) ...
Setting up libk5crypto3:mips64el (1.20.1-1+b1) ...
Setting up libgcc-11-dev:mips64el (11.3.0-12) ...
Setting up libcrypt-dev:mips64el (1:4.4.33-2) ...
Setting up libkrb5-3:mips64el (1.20.1-1+b1) ...
Setting up libgssapi-krb5-2:mips64el (1.20.1-1+b1) ...
Setting up libtirpc3:mips64el (1.3.3+ds-1) ...
Setting up libtirpc-dev:mips64el (1.3.3+ds-1) ...
Setting up libnsl2:mips64el (1.3.0-2) ...
Setting up libnsl-dev:mips64el (1.3.0-2) ...
Setting up libc6-dev:mips64el (2.36-9) ...
Setting up libstdc++-11-dev:mips64el (11.3.0-12) ...
Setting up zlib1g-dev:mips64el (1:1.2.13.dfsg-1) ...
Setting up sbuild-build-depends-main-dummy:mips64el (0.invalid.0) ...
Processing triggers for libc-bin (2.36-9) ...

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

Arch check ok (mips64el included in any)

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

Kernel: Linux 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) amd64 (x86_64)
Toolchain package versions: binutils_2.40-2 dpkg-dev_1.21.21 g++-11_11.3.0-12 g++-12_12.2.0-14 gcc-11_11.3.0-12 gcc-12_12.2.0-14 libc6-dev_2.36-9 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-mips64el-cross_12.2.0-14cross5 libstdc++6_12.2.0-14 libstdc++6-mips64el-cross_12.2.0-14cross5 linux-libc-dev_6.1.20-2
Package versions: adduser_3.132 apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.4 base-passwd_3.6.1 bash_5.2.15-2+b1 binutils_2.40-2 binutils-common_2.40-2 binutils-mips64el-linux-gnuabi64_2.40-2cross2 binutils-x86-64-linux-gnu_2.40-2 bsdextrautils_2.38.1-5+b1 bsdutils_1:2.38.1-5+b1 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-3 cpp-11_11.3.0-12 cpp-12_12.2.0-14 cpp-12-mips64el-linux-gnuabi64_12.2.0-14cross5 cpp-mips64el-linux-gnuabi64_4:12.2.0-4 cross-config_2.6.20 crossbuild-essential-mips64el_12.9 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.4 debian-archive-keyring_2023.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.21 dpkg-cross_2.6.20 dpkg-dev_1.21.21 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 g++_4:12.2.0-3 g++-11_11.3.0-12 g++-12_12.2.0-14 g++-12-mips64el-linux-gnuabi64_12.2.0-14cross5 g++-mips64el-linux-gnuabi64_4:12.2.0-4 gcc_4:12.2.0-3 gcc-11_11.3.0-12 gcc-11-base_11.3.0-12 gcc-12_12.2.0-14 gcc-12-base_12.2.0-14 gcc-12-cross-base-mipsen_12.2.0-14cross5 gcc-12-mips64el-linux-gnuabi64_12.2.0-14cross5 gcc-12-mips64el-linux-gnuabi64-base_12.2.0-14cross5 gcc-9-base_9.5.0-3 gcc-mips64el-linux-gnuabi64_4:12.2.0-4 gettext_0.21-12 gettext-base_0.21-12 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libasan6_11.3.0-12 libasan8_12.2.0-14 libatomic1_12.2.0-14 libatomic1-mips64el-cross_12.2.0-14cross5 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2 libblkid1_2.38.1-5+b1 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-9 libc-dev-bin_2.36-9 libc6_2.36-9 libc6-dev_2.36-9 libc6-dev-mips64el-cross_2.36-8cross2 libc6-mips64el-cross_2.36-8cross2 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-3 libcc1-0_12.2.0-14 libcom-err2_1.47.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2 libctf0_2.40-2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.268 libdebhelper-perl_13.11.4 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.21.21 libelf1_0.188-2.1 libext2fs2_1.47.0-2 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-11-dev_11.3.0-12 libgcc-12-dev_12.2.0-14 libgcc-12-dev-mips64el-cross_12.2.0-14cross5 libgcc-s1_12.2.0-14 libgcc-s1-mips64el-cross_12.2.0-14cross5 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-2 libgomp1_12.2.0-14 libgomp1-mips64el-cross_12.2.0-14cross5 libgpg-error0_1.46-1 libgprofng0_2.40-2 libgssapi-krb5-2_1.20.1-1+b1 libhogweed6_3.8.1-2 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libio-string-perl_1.08-4 libisl23_0.25-1 libitm1_12.2.0-14 libjansson4_2.14-2 libk5crypto3_1.20.1-1+b1 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-1+b1 libkrb5support0_1.20.1-1+b1 liblocale-gettext-perl_1.07-5 liblsan0_12.2.0-14 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5+b1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libnettle8_3.8.1-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libquadmath0_12.2.0-14 libseccomp2_2.5.4-1+b3 libselinux1_3.4-1+b5 libsemanage-common_3.4-1 libsemanage2_3.4-1+b5 libsepol2_3.4-2 libsmartcols1_2.38.1-5+b1 libss2_1.47.0-2 libssl3_3.0.8-1 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-mips64el-cross_12.2.0-14cross5 libstdc++6_12.2.0-14 libstdc++6-mips64el-cross_12.2.0-14cross5 libsub-override-perl_0.09-4 libsystemd0_252.6-1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan0_11.3.0-12 libtsan2_12.2.0-14 libubsan1_12.2.0-14 libuchardet0_0.0.7-1 libudev1_252.6-1 libunistring2_1.0-2 libuuid1_2.38.1-5+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.1+b3 libxxhash0_0.8.1-1 libyaml-perl_1.30-2 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.20-2 linux-libc-dev-mips64el-cross_6.1.8-1cross2 login_1:4.13+dfsg1-1+b1 logsave_1.47.0-2 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 mount_2.38.1-5+b1 ncurses-base_6.4-2 ncurses-bin_6.4-2 passwd_1:4.13+dfsg1-1+b1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-7 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 tzdata_2023c-3 ucf_3.0043+nmu1 usrmerge_35 util-linux_2.38.1-5+b1 util-linux-extra_2.38.1-5+b1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1

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


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

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

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-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

-----BEGIN PGP SIGNATURE-----
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=yj3Z
-----END PGP SIGNATURE-----

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 inline signature for ./plink_1.07+dfsg-4.dsc: no acceptable signature found
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

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.mips64el
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=crossqa
SCHROOT_SESSION_ID=sid-amd64-sbuild-70b1fdf0-e8ee-46d8-aec3-ad9723cc7c32
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa

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

Command: dpkg-buildpackage --sanitize-env -amips64el -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 mips64el-linux-gnuabi64 does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture mips64el
 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=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-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>>'
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from plink.cpp:35:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
In file included from plink.cpp:40:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  196 |     for (int k=0; k<values.size(); k++)
      |                   ~^~~~~~~~~~~~~~
plink.cpp: In function ‘int main(int, char**)’:
plink.cpp:763:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  763 |       par::make_founders &&
      |       ~~~~~~~~~~~~~~~~~~~^~
  764 |       !par::built_families)
      |       ~~~~~~~~~~~~~~~~~~~~
plink.cpp:2106:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2106 |   for (int i=0;i<chrs.size();i++)
      |                ~^~~~~~~~~~~~
plink.cpp: In member function ‘void Plink::cleanUp()’:
plink.cpp:2359:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2359 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
plink.cpp:2362:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2362 |   for (int l=0; l<locus.size(); l++)
      |                 ~^~~~~~~~~~~~~
plink.cpp:2366:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2366 |     for (int l=0; l<SNP.size(); l++)
      |                   ~^~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readData()’:
input.cpp:516:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  516 |               if ( i == include.size() )
      |                    ~~^~~~~~~~~~~~~~~~~
input.cpp:521:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  521 |               if ( i > include.size())
      |                    ~~^~~~~~~~~~~~~~~~
input.cpp:545:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |           if ( gn != 2 * include.size() )
      |                ~~~^~~~~~~~~~~~~~~~~~~~~
input.cpp:579:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  579 |     for (int i=0; i<sample.size(); i++)
      |                   ~^~~~~~~~~~~~~~
input.cpp:595:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  595 |       for (int i=0; i<ambiguous.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~
input.cpp:611:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  611 |   for (int i=0;i<sample.size();i++)
      |                ~^~~~~~~~~~~~~~
input.cpp:631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  631 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readSet()’:
input.cpp:695:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  695 |       for (int i=0; i<snpset.size();i++)
      |                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readClusterFile(bool)’:
input.cpp:787:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  787 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:817:25: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  817 |       if (tokens.size() < 2+par::mult_clst)
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
input.cpp:821:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  821 |               for (int i0=0; i0<tokens.size(); i0++)
      |                              ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readPhenoFile()’:
input.cpp:897:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  897 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:927:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  927 |           for ( int i=2; i<tokens.size(); i++)
      |                          ~^~~~~~~~~~~~~~
input.cpp:961:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  961 |       else if ( ccount != tokens.size() )
      |                 ~~~~~~~^~~~~~~~~~~~~~~~
input.cpp:965:25: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  965 |       if (tokens.size() < 2+par::mult_pheno)
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
input.cpp:1037:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1037 |     for (int i=0; i<sample.size(); i++)
      |                   ~^~~~~~~~~~~~~~
input.cpp:1043:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1043 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:1064:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1064 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::makePhenotype()’:
input.cpp:1208:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1208 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readCovariateFile()’:
input.cpp:1232:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1232 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:1256:25: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1256 |       if (tokens.size() < 2+par::mult_covar)
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
input.cpp:1261:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1261 |             for (int i0=0; i0<tokens.size(); i0++)
      |                            ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readCovListFile()’:
input.cpp:1335:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1335 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:1374:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1374 |       else if (tokens.size() != par::clist_number + 2 )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
input.cpp:1519:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1519 |           for (int c=0; c<covlist.size(); c++)
      |                         ~^~~~~~~~~~~~~~~
input.cpp:1538:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1538 |       for (int c=0; c<covlist.size(); c++)
      |                     ~^~~~~~~~~~~~~~~
input.cpp: In member function ‘bool Plink::readMultiplePhenoFile()’:
input.cpp:1572:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1572 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp:1599:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1599 |       else if (tokens.size() != par::plist_number + 2 )
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
input.cpp:1602:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 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 ‘long unsigned int’} [-Wsign-compare]
 1745 |           for (int c=0; c<phelist.size(); c++)
      |                         ~^~~~~~~~~~~~~~~
input.cpp:1764:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1764 |       for (int c=0; c<phelist.size(); c++)
      |                     ~^~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readSegmentFile(std::ifstream&)’:
input.cpp:1792:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1792 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readMapFile(std::string, std::vector<bool>&, std::vector<int>&, int&)’:
input.cpp:2116:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2116 |   for (int i=0; i<include.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
input.cpp:2172:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2172 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
input.cpp:2200:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2200 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
input.cpp:2210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2210 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
input.cpp:2215:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2215 |   if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
      |                                               ~~~~~~~~~~^~~~~~~~~~~~~~
input.cpp:2225:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2225 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readFamFile(std::string)’:
input.cpp:2389:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2389 |     for (int i=0; i<sample.size(); i++)
      |                   ~^~~~~~~~~~~~~~
input.cpp:2397:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2397 |   for (int i=0;i<sample.size();i++)
      |                ~^~~~~~~~~~~~~~
input.cpp:2419:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2419 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
input.cpp:2453:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2453 |       for (int i=0; i<ambiguous.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::readHomozygSegmentFile(std::ifstream&)’:
input.cpp:2471:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2471 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
input.cpp: In member function ‘void Plink::updateAlleles()’:
input.cpp:2732:12: warning: unused variable ‘success’ [-Wunused-variable]
 2732 |       bool success = false;
      |            ^~~~~~~
input.cpp: In member function ‘void Plink::readData()’:
input.cpp:91:20: warning: ‘PED’ may be used uninitialized [-Wmaybe-uninitialized]
   91 |           if ( feof(PED) )
      |                ~~~~^~~~~
input.cpp:60:10: note: ‘PED’ was declared here
   60 |   FILE * PED;
      |          ^~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
binput.cpp: In member function ‘void Plink::readBinData()’:
binput.cpp:126:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  126 |   for (int i=0; i<locus.size(); i++)
      |                 ~^~~~~~~~~~~~~
binput.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  157 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
binput.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  176 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
binput.cpp:186:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  186 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
binput.cpp:261:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  261 |           while (s<locus.size()) // for all SNPs
      |                  ~^~~~~~~~~~~~~
binput.cpp:339:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  339 |               while (s<locus.size()) // for all SNPs
      |                      ~^~~~~~~~~~~~~
binput.cpp:351:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  351 |                   while (c<7 && s<locus.size())
      |                                 ~^~~~~~~~~~~~~
binput.cpp:398:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  398 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
tinput.cpp: In member function ‘void Plink::readTransposedData()’:
tinput.cpp:161:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |   for (int i=0; i<include.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
tinput.cpp:218:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
tinput.cpp:246:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  246 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
tinput.cpp:256:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  256 |       for (int j=0; j<ordered.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
tinput.cpp:261:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  261 |   if ( (!par::plink) && (!par::run_chr==0) && nl_actual < locus.size() )
      |                                               ~~~~~~~~~~^~~~~~~~~~~~~~
tinput.cpp:271:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  271 |       for(int l=0; l < locus.size(); l++)
      |                    ~~^~~~~~~~~~~~~~
tinput.cpp:309:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  309 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
tinput.cpp:591:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  591 |           if ( c > sample.size())
      |                ~~^~~~~~~~~~~~~~~
tinput.cpp:603:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  603 |       if ( gn != 2 * sample.size() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
genome.cpp: In member function ‘void Plink::calcStratifiedAlleleFreqs()’:
genome.cpp:99:15: 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 ‘long unsigned int’} [-Wsign-compare]
 1227 |   for (int i=0;i<chrs.size();i++)
      |                ~^~~~~~~~~~~~
genome.cpp:1189:7: warning: unused variable ‘win_end’ [-Wunused-variable]
 1189 |   int win_end = win_start + par::prune_ld_win;
      |       ^~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::string display(std::vector<std::__cxx11::basic_string<char> >&)’:
helper.cpp:58:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
helper.cpp: In function ‘std::string displayLine(std::vector<std::__cxx11::basic_string<char> >&)’:
helper.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   66 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
helper.cpp: In function ‘void display(matrix_t&)’:
helper.cpp:76:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   76 |   for (int i=0; i< m.size(); i++)
      |                 ~^~~~~~~~~~
helper.cpp:79:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |       for (int j=0; j<m[i].size(); j++)
      |                     ~^~~~~~~~~~~~
helper.cpp: In function ‘void display(vector_t&)’:
helper.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |   for (int i=0; i< m.size(); i++)
      |                 ~^~~~~~~~~~
helper.cpp: In function ‘void display(std::vector<int>&)’:
helper.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for (int i=0; i< m.size(); i++)
      |                 ~^~~~~~~~~~
helper.cpp: In member function ‘void CArgs::fromPriorLog(std::string)’:
helper.cpp:193:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |       for (int t=0; t<tokens.size(); t++)
      |                     ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > CArgs::value(std::string, int)’:
helper.cpp:267:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |             if ( (i+j) < a.size() )
      |                  ~~~~~~^~~~~~~~~~
helper.cpp:277:16: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  277 |   if (r.size() != c) error("Not enough arguments given for option: "+s+" ");
      |       ~~~~~~~~~^~~~
helper.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > parse2str(std::string)’:
helper.cpp:306:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  306 |   for (int i=0 ; i < s.length() ; i++)
      |                  ~~^~~~~~~~~~~~
helper.cpp:307:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  307 |     if (s[i] == ',' || i == s.length()-1 )
      |                        ~~^~~~~~~~~~~~~~~
helper.cpp:309:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  309 |         if (i == s.length()-1) t += s[i];
      |             ~~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> parse2int(std::string)’:
helper.cpp:323:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  323 |   for (int i=0; i<v.size(); i++)
      |                 ~^~~~~~~~~
helper.cpp: In member function ‘void CArgs::check_unused_options(Plink&)’:
helper.cpp:461:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  461 |   for (int i=1; i<original.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void summaryBasics(Plink&)’:
helper.cpp:595:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  595 |       for (int i=0; i<P.sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~
helper.cpp:611:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  611 |       for (int i=0; i<P.sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘double genotypingRate(Plink&, int)’:
helper.cpp:659:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  659 |       for (int i=0;i<P.sample.size();i++)
      |                    ~^~~~~~~~~~~~~~~~
helper.cpp:664:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  664 |       for (int i=0;i<P.sample.size();i++)
      |                    ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > listPossibleHaplotypes(Plink&, std::vector<int>)’:
helper.cpp:709:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  709 |   while(h<nh)
      |         ~^~~
helper.cpp:729:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  729 |   for (int h=0; h<hap.size(); h++)
      |                 ~^~~~~~~~~~~
helper.cpp: In function ‘void removeMissingPhenotypes(Plink&)’:
helper.cpp:775:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  775 |   for (int i=0; i<P.sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void geno2matrix(std::vector<int>&, matrix_t&, boolmatrix_t&, bool)’:
helper.cpp:795:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  795 |   for (int s = 0 ; s < snps.size() ; s++)
      |                    ~~^~~~~~~~~~~~~
helper.cpp: In function ‘std::string chromosomeName(int)’:
helper.cpp:952:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  952 |   if ( c < 0 || c >= par::chr_code.size() )
      |                 ~~^~~~~~~~~~~~~~~~~~~~~~~
helper.cpp: In function ‘int getMarkerChromosome(Plink&, std::string)’:
helper.cpp:959:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  959 |   for (int i=0;i<P.locus.size();i++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘int getMarkerNumber(Plink&, std::string)’:
helper.cpp:966:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  966 |   for (int i=0;i<P.locus.size();i++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘bool seeChromosome(Plink&, int)’:
helper.cpp:973:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  973 |   for (int l=0;l<P.locus.size();l++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> getChromosomeMarkerRange(Plink&, int)’:
helper.cpp:989:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  989 |   for (int i=0;i<P.locus.size();i++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<int> getChromosomeRange(Plink&)’:
helper.cpp:1040:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1040 |   for (int i=0;i<P.locus.size();i++)
      |                ~^~~~~~~~~~~~~~~
helper.cpp: In function ‘void checkFileExists(std::vector<std::__cxx11::basic_string<char> >)’:
helper.cpp:1172:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1172 |   for (int k=0; k<f.size(); k++)
      |                 ~^~~~~~~~~
helper.cpp: In member function ‘void Plink::prettyPrintLengths()’:
helper.cpp:1264:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1264 |       if (sample[i]->fid.length() > par::pp_maxfid)
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp:1267:35: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1267 |       if (sample[i]->iid.length() > par::pp_maxiid)
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp:1273:33: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1273 |     if (locus[l]->name.length() > par::pp_maxsnp)
      |         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1389:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1389 |           for (int i=0; i<u.size(); i++)
      |                         ~^~~~~~~~~
helper.cpp:1391:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1391 |               for (int j=0; j<u[i].size(); j++)
      |                             ~^~~~~~~~~~~~
helper.cpp: In member function ‘int Plink::deleteSNPs(std::vector<bool>&)’:
helper.cpp:2204:12: warning: unused variable ‘i’ [-Wunused-variable]
 2204 |        int i = 0;
      |            ^
helper.cpp: In member function ‘void Plink::filterOnCovariate()’:
helper.cpp:2455:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2455 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp:2462:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2462 |       for (int j=0; j<filters.size(); j++)
      |                     ~^~~~~~~~~~~~~~~
helper.cpp:2491:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2491 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnCase()’:
helper.cpp:2510:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2510 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnControl()’:
helper.cpp:2530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2530 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnMale()’:
helper.cpp:2549:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2549 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnFemale()’:
helper.cpp:2568:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2568 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnFounder()’:
helper.cpp:2587:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2587 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::filterOnNonFounder()’:
helper.cpp:2606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2606 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
helper.cpp: In member function ‘void Plink::attribFilterSNP()’:
helper.cpp:2638:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2638 |   for (int i=0; i<vlist.size(); i++)
      |                 ~^~~~~~~~~~~~~
helper.cpp:2671:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2671 |       for (int j=1; j<tok.size(); j++)
      |                     ~^~~~~~~~~~~
helper.cpp: In member function ‘void Plink::attribFilterInd()’:
helper.cpp:2722:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2722 |   for (int i=0; i<vlist.size(); i++)
      |                 ~^~~~~~~~~~~~~
helper.cpp:2756:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2756 |       for (int j=1; j<tok.size(); j++)
      |                     ~^~~~~~~~~~~
helper.cpp: In function ‘void makePersonMap(Plink&, std::map<std::__cxx11::basic_string<char>, Individual*>&)’:
helper.cpp:2935:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2935 |   for (int i=0; i<P.sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~
helper.cpp: In function ‘void smoother(Plink&, vector_t&, int, vector_t&, vector_t&, std::vector<int>&)’:
helper.cpp:2959:21: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 2959 |   if ( input.size() != P.nl_all )
      |        ~~~~~~~~~~~~~^~~~~~~~~~~
helper.cpp: In function ‘std::map<std::__cxx11::basic_string<char>, std::set<Range> > readRange(std::string)’:
helper.cpp:3097:20: warning: unused variable ‘s’ [-Wunused-variable]
 3097 |       set<Range> * s;
      |                    ^
helper.cpp: In function ‘void makeScaffold(Plink&)’:
helper.cpp:3324:9: warning: unused variable ‘last’ [-Wunused-variable]
 3324 |     int last = -1;
      |         ^~~~
helper.cpp:3328:9: warning: unused variable ‘thisChromosome’ [-Wunused-variable]
 3328 |     int thisChromosome = P.locus[0]->chr;
      |         ^~~~~~~~~~~~~~
helper.cpp:3329:9: warning: unused variable ‘nextChromosome’ [-Wunused-variable]
 3329 |     int nextChromosome;
      |         ^~~~~~~~~~~~~~
helper.cpp: In member function ‘std::string CArgs::value(std::string)’:
helper.cpp:218:35: warning: control reaches end of non-void function [-Wreturn-type]
  218 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘int CArgs::value_int(std::string)’:
helper.cpp:231:35: warning: control reaches end of non-void function [-Wreturn-type]
  231 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘long unsigned int CArgs::value_lui(std::string)’:
helper.cpp:243:35: warning: control reaches end of non-void function [-Wreturn-type]
  243 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In member function ‘double CArgs::value_double(std::string)’:
helper.cpp:255:35: warning: control reaches end of non-void function [-Wreturn-type]
  255 |   error("Missing an argument for "+s);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘int getInt(std::string, std::string)’:
helper.cpp:378:58: 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:391:58: 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:404:58: warning: control reaches end of non-void function [-Wreturn-type]
  404 |       error("Not valid numeric argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
helper.cpp: In function ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1405:11: warning: ‘maxI’ may be used uninitialized [-Wmaybe-uninitialized]
 1405 |       int maxI;
      |           ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
stats.cpp: In function ‘void tqli(std::vector<double>&, std::vector<double>&, std::vector<std::vector<double> >&)’:
stats.cpp:458:18: warning: unused variable ‘k’ [-Wunused-variable]
  458 |   int m,l,iter,i,k;
      |                  ^
stats.cpp: In function ‘bool svd(matrix_t&, vector_t&, matrix_t&)’:
stats.cpp:813:16: warning: unused variable ‘eps’ [-Wunused-variable]
  813 |   const double eps = 1e-12;
      |                ^~~
stats.cpp:818:7: warning: unused variable ‘r’ [-Wunused-variable]
  818 |   int r = u.size();
      |       ^
stats.cpp: In function ‘std::vector<std::vector<double> > msqrt(std::vector<std::vector<double> >&)’:
stats.cpp:906:16: warning: unused variable ‘eps’ [-Wunused-variable]
  906 |   const double eps = 1e-12;
      |                ^~~
stats.cpp: In function ‘int pca(matrix_t&, boolmatrix_t&, vector_t&, matrix_t&, matrix_t&, bool)’:
stats.cpp:1477:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1477 |         for (int c = 0 ; c < keep.size(); c++)
      |                          ~~^~~~~~~~~~~~~
stats.cpp:1483:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1483 |       for (int c = 0 ; c < keep.size(); c++)
      |                        ~~^~~~~~~~~~~~~
stats.cpp:1515:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1515 |     for (int c = 0 ; c < keep.size(); c++)
      |                      ~~^~~~~~~~~~~~~
stats.cpp:1521:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1521 |   for (int c = 0 ; c < keep.size(); c++)
      |                    ~~^~~~~~~~~~~~~
stats.cpp: In function ‘matrix_t vec2diag(vector_t&)’:
stats.cpp:1531:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1531 |   for (int i = 0; i < v.size(); i++)
      |                   ~~^~~~~~~~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from stats.h:19,
                 from stats.cpp:24:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>]’,
    inlined from ‘bool svdcmp(std::vector<std::vector<double> >&, std::vector<double>&, std::vector<std::vector<double> >&)’ at stats.cpp:1150:15:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘nm’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
stats.cpp: In function ‘bool svdcmp(std::vector<std::vector<double> >&, std::vector<double>&, std::vector<std::vector<double> >&)’:
stats.cpp:1035:22: note: ‘nm’ was declared here
 1035 |   int i,its,j,jj,k,l,nm;
      |                      ^~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
filters.cpp: In member function ‘void Plink::filterSNPs()’:
filters.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   95 |           for (int i=0; i<sample.size(); i++)
      |                         ~^~~~~~~~~~~~~~
filters.cpp:123:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  123 |           for (int i=0;i<sample.size();i++)
      |                        ~^~~~~~~~~~~~~~
filters.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  132 |               for (int l=0; l<locus.size();l++)
      |                             ~^~~~~~~~~~~~~
filters.cpp:155:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  155 |           for (int i=0;i<sample.size();i++)
      |                        ~^~~~~~~~~~~~~~
filters.cpp:163:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |               for (int l=0; l<locus.size();l++)
      |                             ~^~~~~~~~~~~~~
filters.cpp:198:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  198 |           for (int i=0;i<sample.size();i++)
      |                        ~^~~~~~~~~~~~~~
filters.cpp:273:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  273 |               for (int i=0; i<tokens.size(); i++)
      |                             ~^~~~~~~~~~~~~~
filters.cpp:249:14: warning: unused variable ‘freq’ [-Wunused-variable]
  249 |       double freq;
      |              ^~~~
filters.cpp:250:11: warning: unused variable ‘nm’ [-Wunused-variable]
  250 |       int nm;
      |           ^~
filters.cpp:591:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  591 |       for (int i=0; i<hetlist.size(); i++)
      |                     ~^~~~~~~~~~~~~~~
filters.cpp:611:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  611 |       for (int i=0; i<no_founders_found_list.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filters.cpp:739:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  739 |       for ( int l = 0 ; l < locus.size() ; l++ )
      |                         ~~^~~~~~~~~~~~~~
filters.cpp:762:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  762 |           for ( int i = 0 ; i < sample.size() ; i++ )
      |                             ~~^~~~~~~~~~~~~~~
filters.cpp:1078:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1078 |               for (int l=0; l<locus.size();l++)
      |                             ~^~~~~~~~~~~~~
filters.cpp:1091:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1091 |               for (int l=0; l<locus.size();l++)
      |                             ~^~~~~~~~~~~~~
filters.cpp:1143:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1143 |       for (int l=0; l<locus.size(); l++)
      |                     ~^~~~~~~~~~~~~
filters.cpp:1165:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1165 |               for ( int i=0; i<sample.size(); i++)
      |                              ~^~~~~~~~~~~~~~
filters.cpp:1257:7: warning: unused variable ‘tmp’ [-Wunused-variable]
 1257 |   int tmp = deleteSNPs(del);
      |       ^~~
filters.cpp: In member function ‘void Plink::thinSNPs()’:
filters.cpp:1277:7: warning: unused variable ‘x’ [-Wunused-variable]
 1277 |   int x = 0;
      |       ^
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
multi.cpp: In member function ‘std::vector<double> Plink::calcMultiPoint(std::vector<Z>&, Z, std::ofstream&)’:
multi.cpp:295:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  295 |       for (int i=0;i<left.size();i++)
      |                    ~^~~~~~~~~~~~
multi.cpp:304:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  304 |       for (int i=0;i<left.size();i++)
      |                    ~^~~~~~~~~~~~
multi.cpp:357:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Z>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  357 |        for (int i=0;i<right.size();i++)
      |                     ~^~~~~~~~~~~~~
multi.cpp:372:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  372 |    for (int i=0; i<pos.size()-1; i++)
      |                  ~^~~~~~~~~~~~~
multi.cpp:154:8: warning: unused variable ‘is0zero’ [-Wunused-variable]
  154 |   bool is0zero = IBDg.z0 < EPS ? true : false;
      |        ^~~~~~~
multi.cpp:155:8: warning: unused variable ‘is1zero’ [-Wunused-variable]
  155 |   bool is1zero = IBDg.z1 < EPS ? true : false;
      |        ^~~~~~~
mips64el-linux-gnuabi64-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
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
cluster.cpp: In member function ‘void Plink::buildCluster()’:
cluster.cpp:272:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  272 |     for (int z=1; z<=qt.size(); z++)
      |                   ~^~~~~~~~~~~
cluster.cpp:452:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  452 |                   for (int i=0;i<ids.size();i++)
      |                                ~^~~~~~~~~~~
cluster.cpp:511:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  511 |                   for (int i=0;i<val.size();i++)
      |                                ~^~~~~~~~~~~
cluster.cpp:492:15: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  651 |                   for (int i=0;i<tokens.size();i++)
      |                                ~^~~~~~~~~~~~~~
cluster.cpp:784:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  784 |       for (int i=0;i<mdist.size();i++)
      |                    ~^~~~~~~~~~~~~
cluster.cpp:786:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  786 |           for (int j=0;j<mdist.size();j++)
      |                        ~^~~~~~~~~~~~~
cluster.cpp:919:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  919 |         for (int k=0;k<min_dst[0].size();k++)
      |                      ~^~~~~~~~~~~~~~~~~~
cluster.cpp:954:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  954 |       for (int i=0; i<cl.size(); i++)
      |                     ~^~~~~~~~~~
cluster.cpp:955:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  955 |         for (int j=0; j<cl[i].size(); j++)
      |                       ~^~~~~~~~~~~~~
cluster.cpp:975:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  975 |           for (int i=0; i<cl.size()-1; i++)
      |                         ~^~~~~~~~~~~~
cluster.cpp:976:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  976 |             for (int j=i+1; j<cl.size(); j++)
      |                             ~^~~~~~~~~~
cluster.cpp:990:55: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  990 |                         (( cl[i].size()+cl[j].size()) <= par::max_cluster_size) )
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cluster.cpp:1038:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1038 |           for(int j=0;j<cl[jmin].size();j++)
      |                       ~^~~~~~~~~~~~~~~~
cluster.cpp:1041:40: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1041 |           if (cl.size()==1 || cl.size()==par::max_cluster_N) done=true;
      |                               ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
cluster.cpp:1049:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1049 |           for (int i=0; i<cl.size(); i++)
      |                         ~^~~~~~~~~~
cluster.cpp:1050:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1050 |             for (int j=0; j<cl[i].size(); j++)
      |                           ~^~~~~~~~~~~~~
cluster.cpp:1060:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1060 |           for (int j1=0; j1<sol.size(); j1++)
      |                          ~~^~~~~~~~~~~
cluster.cpp:1061:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1061 |             for (int j2=0; j2<sol.size(); j2++)
      |                            ~~^~~~~~~~~~~
cluster.cpp:1107:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1107 |           for (int i=0; i<cl.size(); i++)
      |                         ~^~~~~~~~~~
cluster.cpp:1110:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1110 |               for (int j=0; j<cl[i].size(); j++)
      |                             ~^~~~~~~~~~~~~
cluster.cpp:1133:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1133 |           for (int j=0; j<sol.size(); j++)
      |                         ~^~~~~~~~~~~
cluster.cpp:1163:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1163 |       for (int j=0; j<sol.size(); j++)
      |                     ~^~~~~~~~~~~
cluster.cpp:1169:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1169 |           for (int i=0; i<sol[0].size(); i++)
      |                         ~^~~~~~~~~~~~~~
cluster.cpp: In function ‘double cldist(std::vector<std::vector<double> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1203:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1203 |   for (int i=0; i<a.size(); i++)
      |                 ~^~~~~~~~~
cluster.cpp:1204:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1204 |     for (int j=0; j<b.size(); j++)
      |                   ~^~~~~~~~~
cluster.cpp: In function ‘double groupAvgLink(std::vector<std::vector<double> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1228:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1228 |   for (int i=0; i<a.size(); i++)
      |                 ~^~~~~~~~~
cluster.cpp:1229:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1229 |     for (int j=0; j<b.size(); j++)
      |                   ~^~~~~~~~~
cluster.cpp: In function ‘bool homogeneous_clusters(Plink&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1254:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1254 |   for (int i=0; i<a.size(); i++)
      |                 ~^~~~~~~~~
cluster.cpp:1255:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1255 |     for (int j=0; j<b.size(); j++)
      |                   ~^~~~~~~~~
cluster.cpp: In function ‘bool spec_clusters(Plink&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1272:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1272 |   for (int i=0; i<a.size(); i++)
      |                 ~^~~~~~~~~
cluster.cpp:1276:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1276 |   for (int j=0; j<b.size(); j++)
      |                 ~^~~~~~~~~
cluster.cpp: In function ‘bool pairable_cluster(std::vector<std::vector<bool> >&, std::vector<int>&, std::vector<int>&)’:
cluster.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1290 |   for (int i=0; i<a.size(); i++)
      |                 ~^~~~~~~~~
cluster.cpp:1291:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1291 |     for (int j=0; j<b.size(); j++)
      |                   ~^~~~~~~~~
cluster.cpp: In member function ‘void Plink::groupGenome()’:
cluster.cpp:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1643 |   for ( int i = 4; i<tokens.size(); i++)
      |                    ~^~~~~~~~~~~~~~
cluster.cpp:1661:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1661 |       if ( col_length != tokens.size() )
      |            ~~~~~~~~~~~^~~~~~~~~~~~~~~~
cluster.cpp:1664:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1664 |           for (int i=0;i<tokens.size();i++)
      |                        ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mds.cpp: In member function ‘void Plink::generateMDS()’:
mds.cpp:190:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  190 |                 for (int i1=0; i1<cl[c1].size(); i1++)
      |                                ~~^~~~~~~~~~~~~~
mds.cpp:191:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  191 |                   for (int i2=0; i2<cl[c2].size(); i2++)
      |                                  ~~^~~~~~~~~~~~~~
mds.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  279 |   if ( elist.size() != par::cluster_mds_dim )
      |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
mds.cpp:242:8: warning: unused variable ‘flag’ [-Wunused-variable]
  242 |   bool flag = svd(D,eigenvalue,eigenvector);
      |        ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::displayGenomePV()’:
output.cpp:84:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   84 |   for (int i=0; i<original.size();i++)
      |                 ~^~~~~~~~~~~~~~~~
output.cpp:86:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   86 |       for (int j=0; j<original[i].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~
output.cpp:89:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   89 |           for (int k=0; k<maxr2.size(); k++)
      |                         ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_twolocus()’:
output.cpp:402:28: warning: variable ‘loc1’ set but not used [-Wunused-but-set-variable]
  402 |   vector<Locus*>::iterator loc1 = locus.begin()+m1;
      |                            ^~~~
output.cpp:403:28: warning: variable ‘loc2’ set but not used [-Wunused-but-set-variable]
  403 |   vector<Locus*>::iterator loc2 = locus.begin()+m2;
      |                            ^~~~
output.cpp: In member function ‘void Plink::extractExcludeSet(bool)’:
output.cpp:520:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  520 |       for (int s=0; s<setname.size(); s++)
      |                     ~^~~~~~~~~~~~~~~
output.cpp:526:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  526 |               for (int l=0; l<snpset[s].size(); l++)
      |                             ~^~~~~~~~~~~~~~~~~
output.cpp:553:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  553 |       for (int l=0; l<lst.size(); l++)
      |                     ~^~~~~~~~~~~
output.cpp: In member function ‘void Plink::keep2SetsForGenome()’:
output.cpp:788:7: warning: unused variable ‘n_removed’ [-Wunused-variable]
  788 |   int n_removed = deleteIndividuals(del);
      |       ^~~~~~~~~
output.cpp: In member function ‘void Plink::outputSetFile()’:
output.cpp:2200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2200 |   for (int i=0; i<snpset.size();i++)
      |                 ~^~~~~~~~~~~~~~
output.cpp:2322:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2322 |   for (int j=0; j<inSet.size(); j++)
      |                 ~^~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::setTable()’:
output.cpp:2367:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2367 |   for (int i=0; i < setname.size();i++)
      |                 ~~^~~~~~~~~~~~~~~~
output.cpp:2380:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2380 |       for (int i=0;i<setname.size();i++)
      |                    ~^~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::writeSetFile()’:
output.cpp:2409:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2409 |   for (int j=0; j<snpset.size(); j++)
      |                 ~^~~~~~~~~~~~~~
output.cpp:2412:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2412 |       for (int l=0; l<snpset[j].size(); l++)
      |                     ~^~~~~~~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_pairList()’:
output.cpp:145:61: warning: ‘i2’ may be used uninitialized [-Wmaybe-uninitialized]
  145 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:11: note: ‘i2’ was declared here
  116 |   int i1, i2;
      |           ^~
output.cpp:144:61: warning: ‘i1’ may be used uninitialized [-Wmaybe-uninitialized]
  144 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp:116:7: note: ‘i1’ was declared here
  116 |   int i1, i2;
      |       ^~
output.cpp: In member function ‘void Plink::display_indivReport()’:
output.cpp:69:32: warning: ‘i1’ may be used uninitialized [-Wmaybe-uninitialized]
   69 |          << setw(6) << genotype(*this,i1,l) << "\n";
      |                        ~~~~~~~~^~~~~~~~~~~~
output.cpp:46:7: note: ‘i1’ was declared here
   46 |   int i1;
      |       ^~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
informative.cpp: In member function ‘int Plink::readInformative()’:
informative.cpp:80:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   80 |   for ( int i = 4; i<tokens.size(); i++)
      |                    ~^~~~~~~~~~~~~~
informative.cpp:102:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  102 |       if ( col_length != tokens.size() )
      |            ~~~~~~~~~~~^~~~~~~~~~~~~~~~
informative.cpp:105:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |           for (int i=0;i<tokens.size();i++)
      |                        ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from assoc.cpp:29:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
assoc.cpp: In member function ‘void Plink::calcAssociationWithPermutation(Perm&)’:
assoc.cpp:395:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |           for (int i=0; i<pS->profileSNPs.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:741:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  741 |             for (int j=0; j<pS->selectedSNPs[l].size(); j++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:744:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  744 |                 if ( j < pS->selectedSNPs[l].size() - 1 )
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
assoc.cpp:785:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  785 |       for (int i=0;i<pS->pv_set.size();i++)
      |                    ~^~~~~~~~~~~~~~~~~~
assoc.cpp:788:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  788 |           for (int j=0;j<pS->pv_set[i].size();j++)
      |                        ~^~~~~~~~~~~~~~~~~~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1536:11: warning: unused variable ‘best’ [-Wunused-variable]
 1536 |       int best = 0 ;
      |           ^~~~
assoc.cpp: In member function ‘std::vector<double> Plink::testAssoc(int&, int&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, Perm&, bool)’:
assoc.cpp:1109:68: warning: ‘pvalue’ may be used uninitialized [-Wmaybe-uninitialized]
 1109 |             pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) );
      |                                                               ~~~~~^~~~~~~~~~
assoc.cpp:1019:14: note: ‘pvalue’ was declared here
 1019 |       double pvalue;
      |              ^~~~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/iostream:39,
                 from assoc.cpp:14:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1590:26:
/usr/mips64el-linux-gnuabi64/include/c++/12/ostream:221:25: warning: ‘gen_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:36: note: ‘gen_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |                                    ^~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1697:26:
/usr/mips64el-linux-gnuabi64/include/c++/12/ostream:221:25: warning: ‘rec_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:25: note: ‘rec_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |                         ^~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1672:26:
/usr/mips64el-linux-gnuabi64/include/c++/12/ostream:221:25: warning: ‘dom_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1430:14: note: ‘dom_chisq’ was declared here
 1430 |       double dom_chisq, rec_chisq, gen_chisq;
      |              ^~~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’ at assoc.cpp:1647:26:
/usr/mips64el-linux-gnuabi64/include/c++/12/ostream:221:25: warning: ‘mult_chisq’ may be used uninitialized [-Wmaybe-uninitialized]
  221 |       { return _M_insert(__f); }
      |                ~~~~~~~~~^~~~~
assoc.cpp: In member function ‘std::vector<double> Plink::fullModelAssoc(bool, Perm&)’:
assoc.cpp:1385:22: note: ‘mult_chisq’ was declared here
 1385 |       double mult_p, mult_chisq;
      |                      ^~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
epi.cpp: In member function ‘void Plink::calcEpistasis()’:
epi.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  146 |       for (int e=0;e<snpset[0].size();e++)
      |                    ~^~~~~~~~~~~~~~~~~
epi.cpp:154:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  154 |           for (int e=0;e<snpset[1].size();e++)
      |                        ~^~~~~~~~~~~~~~~~~
epi.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |           for (int e=0;e<snpset[0].size();e++)
      |                        ~^~~~~~~~~~~~~~~~~
epi.cpp:438:26: warning: unused variable ‘zero’ [-Wunused-variable]
  438 |                   double zero = 0;
      |                          ^~~~
epi.cpp:701:11: warning: unused variable ‘c’ [-Wunused-variable]
  701 |       int c=0;
      |           ^
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from prephap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::readTagFile()’:
prephap.cpp:226:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  470 |           for (int s=0;s<S.size();s++)
      |                        ~^~~~~~~~~
prephap.cpp: In member function ‘void HaploPhase::makeSlidingWindow(std::string)’:
prephap.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int i=0; i<tok.size(); i++)
      |                 ~^~~~~~~~~~~
prephap.cpp:560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  560 |   for (int i=0; i<spec.size(); i++)
      |                 ~^~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from phase.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from phase.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
phase.cpp: In member function ‘vector_t HaploPhase::phaseAllHaplotypes(bool, Perm&)’:
phase.cpp:373:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  373 |               for (int i=0; i<t.size(); i++)
      |                             ~^~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::enumerateHaplotypes(std::vector<int>&)’:
phase.cpp:472:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  472 |   while (h<nh)
      |          ~^~~
phase.cpp: In member function ‘void HaploPhase::performAlternEM()’:
phase.cpp:678:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  678 |                       for (int z=0; z<currentStub.size(); z++)
      |                                     ~^~~~~~~~~~~~~~~~~~~
phase.cpp:1187:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::vector<int>, int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1187 |       if ( nh != hapmap.size() )
      |            ~~~^~~~~~~~~~~~~~~~
phase.cpp:1238:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1238 |           for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1280:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1280 |               for (int z=0; z<hap1[i].size(); z++)
      |                             ~^~~~~~~~~~~~~~~
phase.cpp:1299:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1299 |           for (int z=0; z<hap1[par::haplo_plem_follow_ind].size(); z++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phase.cpp:1575:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1575 |                   for ( int z = 0 ; z < pp[i].size() ; z++ )
      |                                     ~~^~~~~~~~~~~~~~
phase.cpp: In member function ‘void HaploPhase::prunePhase(int)’:
phase.cpp:1829:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1829 |   for (int z=0; z < hap1[i].size(); z++)
      |                 ~~^~~~~~~~~~~~~~~~
phase.cpp:1843:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1843 |       for (int z=0; z < new_pp.size(); z++)
      |                     ~~^~~~~~~~~~~~~~~
phase.cpp: In member function ‘double HaploPhase::dosage(int, std::set<int>&)’:
phase.cpp:1888:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1888 |       for (int z = 0; z < h1.size(); z++)
      |                       ~~^~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
trio.cpp: In function ‘void addPerson(Family*, Individual*)’:
trio.cpp:91:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   91 |   for (int c=0; c<f->kid.size(); c++)
      |                 ~^~~~~~~~~~~~~~
trio.cpp: In member function ‘void Plink::parseTrios()’:
trio.cpp:258:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  258 |               for (int k=0; k<mf->kid.size(); k++)
      |                             ~^~~~~~~~~~~~~~~
trio.cpp:272:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  272 |               for (int k=0; k<mf->kid.size(); k++)
      |                             ~^~~~~~~~~~~~~~~
trio.cpp:335:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  335 |                 for (int k=0; k < (*f)->kid.size() ;k++)
      |                               ~~^~~~~~~~~~~~~~~~~~
trio.cpp:342:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  342 |               for ( int k=0; k<(*f)->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~~
trio.cpp:350:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  350 |               for ( int k=0; k<(*f)->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~~
trio.cpp: In member function ‘void Plink::checkMendel()’:
trio.cpp:469:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  469 |   for (int f=0; f<family.size(); f++)
      |                 ~^~~~~~~~~~~~~~
trio.cpp:474:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  474 |   for (int f=0; f<family.size(); f++)
      |                 ~^~~~~~~~~~~~~~
trio.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  492 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
trio.cpp:504:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  504 |           for (int c=0; c<kid.size(); c++)
      |                         ~^~~~~~~~~~~
trio.cpp:871:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  871 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
trio.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  882 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
trio.cpp:895:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  895 |               for (int c=0; c<kid.size(); c++)
      |                             ~^~~~~~~~~~~
trio.cpp:931:13: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1038 |   for (int f=0; f<family.size(); f++)
      |                 ~^~~~~~~~~~~~~~
trio.cpp:1048:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1048 |       for (int c=0; c<kid.size(); c++)
      |                     ~^~~~~~~~~~~
trio.cpp: In member function ‘void Plink::makeMissingParents()’:
trio.cpp:1236:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1236 |           for ( int k=0; k<person->pm->kids.size(); k++)
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
trio.cpp:1245:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1245 |           for ( int k=0; k<person->pp->kids.size(); k++)
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
tdt.cpp: In member function ‘void Plink::perm_testTDT(Perm&)’:
tdt.cpp:81:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |           for (int i=0; i<klist[k]->person.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:96:30: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  210 |           for (int i=0; i<pS->profileSNPs.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:234:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  234 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
tdt.cpp:327:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  327 |             for (int j=0; j<pS->selectedSNPs[l].size(); j++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:330:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  330 |                 if ( j < pS->selectedSNPs[l].size() - 1 )
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tdt.cpp:412:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  412 |       for (int i=0;i<pS->pv_set.size();i++)
      |                    ~^~~~~~~~~~~~~~~~~~
tdt.cpp:415:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  415 |           for (int j=0;j<pS->pv_set[i].size();j++)
      |                        ~^~~~~~~~~~~~~~~~~~~~~
tdt.cpp: In member function ‘std::vector<double> Plink::testTDT(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
tdt.cpp:522:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  522 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
tdt.cpp:557:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  557 |           for (int c=0; c<kid.size(); c++)
      |                         ~^~~~~~~~~~~
tdt.cpp:668:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  668 |           for (int f=0; f<family.size(); f++)
      |                         ~^~~~~~~~~~~~~~
tdt.cpp:776:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  776 |           for (int f=0; f<family.size(); f++)
      |                         ~^~~~~~~~~~~~~~
tdt.cpp:937:55: warning: ‘zt’ may be used uninitialized [-Wmaybe-uninitialized]
  937 |                   double OR_upper = exp( log(OR) + zt * sqrt(1/t1+1/t2)) ;
      |                                                    ~~~^~~~~~~~~~~~~~~~~
tdt.cpp:460:10: note: ‘zt’ was declared here
  460 |   double zt;
      |          ^~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
sharing.cpp: In member function ‘void Plink::perm_sharingIBSTest(Perm&)’:
sharing.cpp:102:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  102 |   for (int l=0; l<snpset.size(); l++)
      |                 ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
genepi.cpp: In function ‘double C(int, double, double)’:
genepi.cpp:78:1: warning: no return statement in function returning non-void [-Wreturn-type]
   78 | }
      | ^
genepi.cpp: In function ‘long double pillai(int, int, int, double)’:
genepi.cpp:169:1: warning: no return statement in function returning non-void [-Wreturn-type]
  169 | }
      | ^
genepi.cpp: In member function ‘void Plink::driverSCREEPI()’:
genepi.cpp:334:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  334 |   for (int s=0; s<snpset.size(); s++)
      |                 ~^~~~~~~~~~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:489:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  489 |             for (int l=0; l<P.snpset[s1].size(); l++)
      |                           ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:497:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  497 |             for (int l=0; l<P.snpset[s2].size(); l++)
      |                           ~^~~~~~~~~~~~~~~~~~~~
genepi.cpp:506:17: 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 ‘long 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 ‘long 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;
      |        ^~~~~~~~~~~~~~~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from /usr/mips64el-linux-gnuabi64/include/c++/12/functional:62,
                 from genepi.cpp:20:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator<int>]’,
    inlined from ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’ at genepi.cpp:855:84:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘cancor1_pos’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
genepi.cpp: In function ‘void CCA_logit(bool, std::vector<std::vector<int> >&, Set&, Plink&)’:
genepi.cpp:614:17: note: ‘cancor1_pos’ was declared here
  614 |             int cancor1_pos;
      |                 ^~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from sets.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
sets.cpp: In member function ‘void Set::sizeSets()’:
sets.cpp:37:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |   for(int s=0;s<snpset.size();s++)
      |               ~^~~~~~~~~~~~~~
sets.cpp:52:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   52 |       for(int i=0;i<snpset.size();i++)
      |                   ~^~~~~~~~~~~~~~
sets.cpp:59:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   59 |           else if (par::set_min > snpset[i].size() )
      |                    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
sets.cpp:62:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   62 |           if (par::set_max==-1 || par::set_max > snpset[i].size() )
      |                                   ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneSets(Plink&)’:
sets.cpp:99:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   99 |   for(int i=0;i<snpset.size();i++)
      |               ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::pruneMC(Plink&, bool, double)’:
sets.cpp:129:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  129 |   for (int s=0; s<snpset.size(); s++)
      |                 ~^~~~~~~~~~~~~~
sets.cpp:176:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  176 |       for (int s=0; s<snpset.size(); s++)
      |                     ~^~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::dropNotSet(Plink&)’:
sets.cpp:216:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  216 |   for (int i=0;i<snpset.size();i++)
      |                ~^~~~~~~~~~~~~~
sets.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |       for (int j=0; j < snpset[i].size(); j++)
      |                     ~~^~~~~~~~~~~~~~~~~~
sets.cpp:236:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |   for (int i=0;i<snpset.size();i++)
      |                ~^~~~~~~~~~~~~~
sets.cpp:237:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |     for (int j=0; j < snpset[i].size(); j++)
      |                   ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::makeLDSets()’:
sets.cpp:317:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  317 |   for (int i=0;i<snpset.size();i++)
      |                ~^~~~~~~~~~~~~~
sets.cpp:323:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  323 |       for (int j=0; j < snpset[i].size(); j++)
      |                     ~~^~~~~~~~~~~~~~~~~~
sets.cpp:329:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  329 |       for (int j=0; j < snpset[i].size(); j++)
      |                     ~~^~~~~~~~~~~~~~~~~~
sets.cpp:332:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  332 |           for (int k=j+1; k < snpset[i].size(); k++)
      |                           ~~^~~~~~~~~~~~~~~~~~
sets.cpp:367:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |       for (int i=0;i<snpset.size();i++)
      |                    ~^~~~~~~~~~~~~~
sets.cpp:370:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  370 |           for (int j=0; j < snpset[i].size(); j++)
      |                         ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::initialiseSetMapping()’:
sets.cpp:412:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  412 |   for (int i=0;i<snpset.size();i++)
      |                ~^~~~~~~~~~~~~~
sets.cpp:413:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  413 |     for (int j=0; j < snpset[i].size(); j++)
      |                   ~~^~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘void Set::empiricalSetPValues()’:
sets.cpp:618:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  618 |       for (int i=0;i<stat_set.size();i++)
      |                    ~^~~~~~~~~~~~~~~~
sets.cpp:619:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  619 |         for (int j=0;j<stat_set[i].size();j++)
      |                      ~^~~~~~~~~~~~~~~~~~~
sets.cpp:631:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  631 |       for (int i=0;i<pv_set.size();i++)
      |                    ~^~~~~~~~~~~~~~
sets.cpp:632:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  632 |         for (int j=0;j<pv_set[i].size();j++)
      |                      ~^~~~~~~~~~~~~~~~~
sets.cpp:642:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  642 |       for (int i=0;i<pv_set.size();i++)
      |                    ~^~~~~~~~~~~~~~
sets.cpp:643:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  643 |         for (int j=0;j<pv_set[i].size();j++)
      |                      ~^~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::profileTestScore()’:
sets.cpp:703:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  703 |   for (int i=0; i<snpset.size(); i++)
      |                 ~^~~~~~~~~~~~~~
sets.cpp:713:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  713 |       for (int j=0; j<profileSNPs[i].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitLDSetTest(vector_t&, bool)’:
sets.cpp:905:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  905 |   for (int i=0; i<snpset.size(); i++)
      |                 ~^~~~~~~~~~~~~~
sets.cpp:975:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  975 |           for (int k=0; k<selected.size(); k++)
      |                         ~^~~~~~~~~~~~~~~~
sets.cpp: In member function ‘vector_t Set::fitStepwiseModel()’:
sets.cpp:1042:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1042 |   for (int i=0; i<snpset.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::permuteInCluster()’:
perm.cpp:144:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |   for (int j=0; j<s.size(); j++)
      |                 ~^~~~~~~~~
perm.cpp:145:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  145 |     for (int k=0; k<s[j].size(); k++)
      |                   ~^~~~~~~~~~~~
perm.cpp: In member function ‘void Perm::setOriginalRanking(vector_t&)’:
perm.cpp:187:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  187 |   for (int i=0; i<original.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~
perm.cpp:199:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  199 |   for(int i=0; i<original.size(); i++)
      |                ~^~~~~~~~~~~~~~~~
perm.cpp: In member function ‘bool Perm::update(std::vector<double>&, std::vector<double>&)’:
perm.cpp:273:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  273 |                           for (int j=0;j< P.pS->snpset[l].size();j++)
      |                                        ~^~~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_IxJxK(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:747:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  747 |   for (int i=0; i<X.size(); i++)
      |                 ~^~~~~~~~~
mh.cpp: In member function ‘std::vector<double> Plink::calcMantelHaenszel_ORD(std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
mh.cpp:1249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1249 |   for (int i=0; i<X.size(); i++)
      |                 ~^~~~~~~~~
mh.cpp:1312:1: warning: no return statement in function returning non-void [-Wreturn-type]
 1312 | }
      | ^
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::preGeneDrop()’:
genedrop.cpp:64:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   64 |   for (int i=0; i<P.sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~
genedrop.cpp: In member function ‘void Perm::dropAlleles(Plink&, Individual*, int, int, std::vector<bool>&, std::vector<bool>&, std::vector<bool>&, std::map<Individual*, int>&)’:
genedrop.cpp:340:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  340 |   for (int k=0; k<person->kids.size(); k++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
merge.cpp: In member function ‘void Plink::mergeData()’:
merge.cpp:333:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  333 |   for (int i=0; i<include.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
merge.cpp:377:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  377 |   for (int l=0; l<locus2.size(); l++)
      |                 ~^~~~~~~~~~~~~~
merge.cpp:395:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int l=0;l<locus.size();l++)
      |                ~^~~~~~~~~~~~~
merge.cpp:403:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  403 |        for (int l=0;l<locus.size();l++)
      |                     ~^~~~~~~~~~~~~
merge.cpp:426:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  426 |       for (int i=0; i<locus2.size()-exist_cnt; i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~
merge.cpp:722:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  722 |           if ( i > include.size())
      |                ~~^~~~~~~~~~~~~~~~
merge.cpp:733:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  733 |       if ( gn != 2 * include.size() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~~
merge.cpp:784:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  784 |     for (int i=0; i<sample.size(); i++)
      |                   ~^~~~~~~~~~~~~~
merge.cpp:830:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  830 |       for (int i=0;i<sample.size();i++)
      |                    ~^~~~~~~~~~~~~~
merge.cpp:842:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  842 |           for (int i=0; i<sample.size(); i++)
      |                         ~^~~~~~~~~~~~~~
merge.cpp: In member function ‘bool Plink::reconcileMerge(int, int, std::string, std::string, bool, bool, std::ofstream&, std::map<std::__cxx11::basic_string<char>, int>&)’:
merge.cpp:1103:3: warning: ‘write’ may be used uninitialized [-Wmaybe-uninitialized]
 1103 |   if (write)
      |   ^~
merge.cpp:943:8: note: ‘write’ was declared here
  943 |   bool write;
      |        ^~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
hotel.cpp: In member function ‘void Plink::perm_testHotel(Perm&)’:
hotel.cpp:77:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   77 |     if (!sample[i]->missing)
      |        ^
hotel.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  173 |   for (int s=0; s<snpset.size(); s++)
      |                 ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
multiple.cpp: In member function ‘void Plink::multcomp(std::vector<double>&, std::string)’:
multiple.cpp:85:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   85 |   for (int l=0; l<chi.size(); l++)
      |                 ~^~~~~~~~~~~
multiple.cpp:131:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Pair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  131 |   for (int i=0; i<schi.size(); i++)
      |                 ~^~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from haploCC.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
haploCC.cpp: In member function ‘void HaploPhase::haplotypicCC(std::map<int, int>&, int, bool)’:
haploCC.cpp:48:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |               for (int z = 0 ; z < hap1[i].size(); z++)
      |                                ~~^~~~~~~~~~~~~~~~
haploCC.cpp:62:41: 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 ‘long 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 ‘long 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 ‘long 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 ) )
      |                                        ~~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from haploTDT.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘void Plink::perm_testTDT_POO(Perm&)’:
poo.cpp:93:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   93 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
poo.cpp:195:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<double> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  195 |       for (int i=0;i<pS->pv_set.size();i++)
      |                    ~^~~~~~~~~~~~~~~~~~
poo.cpp:198:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  198 |           for (int j=0;j<pS->pv_set[i].size();j++)
      |                        ~^~~~~~~~~~~~~~~~~~~~~
poo.cpp: In member function ‘std::vector<double> Plink::testTDT_POO(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
poo.cpp:293:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  293 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
poo.cpp:328:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  328 |           for (int c=0; c<kid.size(); c++)
      |                         ~^~~~~~~~~~~
poo.cpp:239:10: warning: unused variable ‘zt’ [-Wunused-variable]
  239 |   double zt;
      |          ^~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
webcheck.cpp: In member function ‘void Plink::webcheck(CArgs&)’:
webcheck.cpp:117:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  117 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
webcheck.cpp:130:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  180 |           if ( i < tokens.size() - 1)
      |                ~~^~~~~~~~~~~~~~~~~~~
webcheck.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
qfam.cpp: In function ‘void scoreBetween(Plink&, int)’:
qfam.cpp:82:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   82 |               for (int k=0; k < (*f)->kid.size() ;k++)
      |                             ~~^~~~~~~~~~~~~~~~~~
qfam.cpp:89:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   89 |               for ( int k=0; k<(*f)->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~~
qfam.cpp:97:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   97 |               for ( int k=0; k<(*f)->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~~
qfam.cpp: In member function ‘void Plink::perm_testQTDT(Perm&)’:
qfam.cpp:267:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int i=0; i < family.size(); i++)
      |                 ~~^~~~~~~~~~~~~~~
qfam.cpp:315:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |   for (int f = 0 ; f < family.size() ; f++)
      |                    ~~^~~~~~~~~~~~~~~
qfam.cpp: In member function ‘vector_t Plink::calcQTDT(std::vector<int>&, std::ofstream&, bool, Perm&, std::vector<int>&, std::vector<bool>&)’:
qfam.cpp:505:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  505 |              for ( int k = 0 ; k < (*f)->kid.size() ; k++)
      |                                ~~^~~~~~~~~~~~~~~~~~
qfam.cpp:648:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  648 |          for (int i=0; i<family.size(); i++)
      |                        ~^~~~~~~~~~~~~~
qfam.cpp:657:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  657 |          for (int f=0; f<pbetween.size(); f++)
      |                        ~^~~~~~~~~~~~~~~~
qfam.cpp:639:10: warning: unused variable ‘tc’ [-Wunused-variable]
  639 |      int tc = 0;
      |          ^~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
linear.cpp: In member function ‘virtual void LinearModel::pruneY()’:
linear.cpp:50:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   50 |   for (int i=0; i<Y.size(); i++)
      |                 ~^~~~~~~~~
linear.cpp: In member function ‘double LinearModel::getPValue()’:
linear.cpp:734:8: warning: unused variable ‘okay’ [-Wunused-variable]
  734 |   bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid;
      |        ^~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from linear.h:17,
                 from linear.cpp:18:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = std::vector<double>; _Alloc = std::allocator<std::vector<double> >]’,
    inlined from ‘void gaussj(matrix_t&, matrix_t&)’ at linear.cpp:97:36:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘irow’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
linear.cpp: In function ‘void gaussj(matrix_t&, matrix_t&)’:
linear.cpp:75:14: note: ‘irow’ was declared here
   75 |   int i,icol,irow,j,k,l,ll;
      |              ^~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = std::vector<double>; _Alloc = std::allocator<std::vector<double> >]’,
    inlined from ‘void gaussj(matrix_t&, matrix_t&)’ at linear.cpp:102:15:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘icol’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
linear.cpp: In function ‘void gaussj(matrix_t&, matrix_t&)’:
linear.cpp:75:9: note: ‘icol’ was declared here
   75 |   int i,icol,irow,j,k,l,ll;
      |         ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
bmerge.cpp: In member function ‘void Plink::mergeBinaryData()’:
bmerge.cpp:90:16: warning: variable ‘inc’ set but not used [-Wunused-but-set-variable]
   90 |       long int inc;
      |                ^~~
bmerge.cpp:357:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  357 |   for (int i=0; i<ordered.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
bmerge.cpp:390:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  390 |   for (int l=0; l<locus2.size(); l++)
      |                 ~^~~~~~~~~~~~~~
bmerge.cpp:409:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  409 |   for (int l=0;l<locus.size();l++)
      |                ~^~~~~~~~~~~~~
bmerge.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  417 |        for (int l=0;l<locus.size();l++)
      |                     ~^~~~~~~~~~~~~
bmerge.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |       for (int i=0; i<locus2.size()-exist_cnt; i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~
bmerge.cpp:549:11: warning: variable ‘indn’ set but not used [-Wunused-but-set-variable]
  549 |       int indn = isample->second;
      |           ^~~~
bmerge.cpp:697:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  697 |       while (s<locus2.size()) // for all SNPs in second file
      |              ~^~~~~~~~~~~~~~
bmerge.cpp:692:14: warning: unused variable ‘snp’ [-Wunused-variable]
  692 |       CSNP * snp;
      |              ^~~
bmerge.cpp:839:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  839 |     for (int i=0; i<sample.size(); i++)
      |                   ~^~~~~~~~~~~~~~
bmerge.cpp:871:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  871 |       for (int i=0;i<sample.size();i++)
      |                    ~^~~~~~~~~~~~~~
bmerge.cpp:883:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  883 |           for (int i=0; i<sample.size(); i++)
      |                         ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
parse.cpp: In function ‘void setOptions(CArgs&)’:
parse.cpp:80:6: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
   80 | void setOptions(CArgs & a)
      |      ^~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from mishap.cpp:20:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
mishap.cpp: In member function ‘void Plink::performMisHapTests()’:
mishap.cpp:209:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  209 |                       for (int z = 0 ; z < haplo->hap1[i].size(); z++)
      |                                        ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:236:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |                       for (int z = 0 ; z < haplo->hap1[i].size(); z++)
      |                                        ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:349:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  349 |               for (int z = 0 ; z < haplo->hap1[i].size(); z++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
mishap.cpp:373:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  373 |               for (int z = 0 ; z < haplo->hap1[i].size(); z++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
legacy.cpp: In member function ‘void Plink::calcRegression(int)’:
legacy.cpp:368:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  368 |   for (int i=0; i<pair1.size(); i++)
      |                 ~^~~~~~~~~~~~~
legacy.cpp:377:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  377 |       for (int i=0;i<v_pihat.size();i++)
      |                    ~^~~~~~~~~~~~~~~
legacy.cpp:381:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  381 |       for (int i=0;i<pihat.size();i++)
      |                    ~^~~~~~~~~~~~~
legacy.cpp:384:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  384 |           for (int j=0;j<pihat[i].size();j++)
      |                        ~^~~~~~~~~~~~~~~~
legacy.cpp:390:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  390 |       for (int i=0;i<phenotype.size();i++)
      |                    ~^~~~~~~~~~~~~~~~~
legacy.cpp:395:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |       for (int i=0;i<pihat_G.size();i++)
      |                    ~^~~~~~~~~~~~~~~
legacy.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  415 |   for (int i=0; i<in_anal.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
legacy.cpp:424:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  424 |   for (int i=0; i<in_anal.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
legacy.cpp:460:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  460 |       for (int j=0; j<s.size(); j++)
      |                     ~^~~~~~~~~
legacy.cpp:461:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  461 |         for (int k=0; k<s[j].size(); k++)
      |                       ~^~~~~~~~~~~~
legacy.cpp:462:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  462 |           for (int i=0; i<pin_anal.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~
legacy.cpp:467:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  467 |       for (int i=0; i<in_anal.size(); i++)
      |                     ~^~~~~~~~~~~~~~~
legacy.cpp:480:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  480 |       for (int i=0; i<pair1.size(); i++)
      |                     ~^~~~~~~~~~~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from plink.h:21,
                 from legacy.cpp:21:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Locus*; _Alloc = std::allocator<Locus*>]’,
    inlined from ‘void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)’ at legacy.cpp:206:51:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
legacy.cpp: In member function ‘void Plink::findIBSRuns(Individual*, Individual*, std::ofstream&)’:
legacy.cpp:35:7: note: ‘last’ was declared here
   35 |   int last;
      |       ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
homozyg.cpp: In function ‘void displayPoolVerbose(Plink&, Pool*, std::ofstream&)’:
homozyg.cpp:673:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  673 |   for (int i=0; i < plist.size(); i++)
      |                 ~~^~~~~~~~~~~~~~
homozyg.cpp:695:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  695 |   for (int i=0; i < plist.size(); i++)
      |                 ~~^~~~~~~~~~~~~~
homozyg.cpp:722:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  722 |       for (int i=0; i < plist.size(); i++)
      |                     ~~^~~~~~~~~~~~~~
homozyg.cpp:756:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  756 |       for (int i=0; i < plist.size(); i++)
      |                     ~~^~~~~~~~~~~~~~
homozyg.cpp:773:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  773 |       for (int i=0; i < plist.size(); i++)
      |                     ~~^~~~~~~~~~~~~~
homozyg.cpp:861:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  861 |           for (int i=0; i < plist.size(); i++)
      |                         ~~^~~~~~~~~~~~~~
homozyg.cpp: In member function ‘void Plink::summariseHomoRuns()’:
homozyg.cpp:1134:34: warning: comparison of integer expressions of different signedness: ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1134 |       if ( thispool->segs.size() >= par::pool_size_min )
      |            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1178:38: warning: comparison of integer expressions of different signedness: ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1178 |           if ( thispool->segs.size() >= par::pool_size_min )
      |                ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1331:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set<Segment*, std::less<Segment*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1331 |       for (int i=0; i< (*pA)->segs.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1437:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1437 |           for (int i=0; i < (*pA)->group.size() ; i++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp:1441:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1441 |                   if ( (*pA)->match[i].size() >= maxlist )
      |                        ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
homozyg.cpp:1461:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1461 |           for (int i=0; i < (*pA)->group.size() ; i++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~
homozyg.cpp: In member function ‘void Plink::findHomoWindow(Individual*, std::ofstream&)’:
homozyg.cpp:2155:27: warning: value computed is not used [-Wunused-value]
 2155 |         homozygWindows[l] == 0;
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::segmentPermutationTest(Perm&, bool, std::string, std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
segment.cpp:871:9: 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 ‘long unsigned int’} [-Wsign-compare]
 1529 |   for (int i=0;i<pihat.size();i++)
      |                ~^~~~~~~~~~~~~
segment.cpp: In member function ‘void Plink::indivSegmentSummary()’:
segment.cpp:1855:21: 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 )
      |                     ~~~~~~~~~~~~~^~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from model.cpp:17:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
model.cpp: In member function ‘void Model::setMissing(std::vector<bool>&)’:
model.cpp:132:23: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  132 |   if ( include.size() != P->n )
      |        ~~~~~~~~~~~~~~~^~~~~~~
model.cpp: In member function ‘void Model::buildDesignMatrix()’:
model.cpp:354:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  354 |       for (int i=0; i< par::parameter_list.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:367:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |       for ( int i = 0 ; i < X.size() ; i++)
      |                         ~~^~~~~~~~~~
model.cpp:374:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  374 |           for ( int j = 0 ; j < par::parameter_list.size() ; j++)
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp: In member function ‘bool Model::checkVIF()’:
model.cpp:613:10: warning: unused variable ‘maxVIF’ [-Wunused-variable]
  613 |   double maxVIF = 0;
      |          ^~~~~~
model.cpp: In member function ‘double Model::buildQFAM(Individual*)’:
model.cpp:849:10: warning: control reaches end of non-void function [-Wreturn-type]
  849 |     error("Internal problem with QFAM model specification");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
logistic.cpp: In member function ‘virtual void LogisticModel::pruneY()’:
logistic.cpp:66:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   66 |   for (int i=0; i<Y.size(); i++)
      |                 ~^~~~~~~~~
logistic.cpp: In member function ‘double LogisticModel::getPValue()’:
logistic.cpp:327:8: warning: unused variable ‘okay’ [-Wunused-variable]
  327 |   bool okay = var[testParameter] < 1e-20 || !realnum(var[testParameter]) ? false : all_valid;
      |        ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from glm.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
glm.cpp: In member function ‘vector_t Plink::glmAssoc(bool, Perm&)’:
glm.cpp:294:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  294 |           for (int h=1; h < whap->current->group.size(); h++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
glm.cpp:344:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |               for (int c=0; c<conditioner.size(); c++)
      |                             ~^~~~~~~~~~~~~~~~~~~
glm.cpp:355:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  355 |               for (int c=0; c<conditioner.size(); c++)
      |                             ~^~~~~~~~~~~~~~~~~~~
glm.cpp:423:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  423 |           for (int c=0; c<conditioner.size(); c++)
      |                         ~^~~~~~~~~~~~~~~~~~~
glm.cpp:610:35: warning: ‘df’ may be used uninitialized [-Wmaybe-uninitialized]
  610 |           double pvalue = chiprobP(chisq,df);
      |                           ~~~~~~~~^~~~~~~~~~
glm.cpp:556:15: note: ‘df’ was declared here
  556 |           int df;
      |               ^~
mips64el-linux-gnuabi64-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;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In function ‘void displayScoresRegion(std::ofstream&, RCount&)’:
elf.cpp:493:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  493 |       for ( int k = 0 ; k < i->second.size(); k++)
      |                         ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘void Plink::permTestRareDistribution(Perm&)’:
elf.cpp:609:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |   for (int l=0; l< original.size(); l++)
      |                 ~^~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘vector_t Plink::testRareDistribution(Perm&, bool, std::map<Range, int2>&)’:
elf.cpp:654:16: warning: unused variable ‘pthresh’ [-Wunused-variable]
  654 |   const double pthresh = 0.01;
      |                ^~~~~~~
elf.cpp:655:8: warning: unused variable ‘one_sided’ [-Wunused-variable]
  655 |   bool one_sided = true;
      |        ^~~~~~~~~
elf.cpp:707:7: warning: unused variable ‘srange_cnt’ [-Wunused-variable]
  707 |   int srange_cnt = 0;
      |       ^~~~~~~~~~
elf.cpp:708:8: warning: unused variable ‘inRange’ [-Wunused-variable]
  708 |   bool inRange = false;
      |        ^~~~~~~
elf.cpp: In member function ‘void Plink::displayRareRange()’:
elf.cpp:895:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  895 |   for (int i = 0 ; i < tokens.size() ; i++)
      |                    ~~^~~~~~~~~~~~~~~
elf.cpp:939:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  939 |       if ( tokens.size() != ncol )
      |            ~~~~~~~~~~~~~~^~~~~~~
elf.cpp: In member function ‘bool RCount::addSNP(int)’:
elf.cpp:374:10: warning: ‘wt’ may be used uninitialized [-Wmaybe-uninitialized]
  374 |   double wt;
      |          ^~
elf.cpp: In member function ‘void Plink::elfBaseline()’:
elf.cpp:1142:15: warning: ‘p_gcnt’ may be used uninitialized [-Wmaybe-uninitialized]
 1142 |               ++(*p_gcnt);
      |               ^~~~~~~~~~~
elf.cpp:1112:13: note: ‘p_gcnt’ was declared here
 1112 |       int * p_gcnt;
      |             ^~~~~~
elf.cpp:1165:22: warning: ‘p_cnt’ may be used uninitialized [-Wmaybe-uninitialized]
 1165 |                   ++(*p_cnt);
      |                     ~^~~~~~~
elf.cpp:1111:13: note: ‘p_cnt’ was declared here
 1111 |       int * p_cnt;
      |             ^~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
dfam.cpp: In member function ‘std::vector<double> Plink::testSibTDT(bool, bool, Perm&, std::vector<bool>&, std::vector<bool>&)’:
dfam.cpp:76:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   76 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
dfam.cpp:86:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   86 |               for ( int k=0; k<fam->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~
dfam.cpp:96:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   96 |               for ( int k=0; k<fam->kid.size(); k++)
      |                              ~^~~~~~~~~~~~~~~~
dfam.cpp:106:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  106 |             for (int c=0; c<klist[k]->person.size(); c++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Family*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  157 |       for (int f=0; f<family.size(); f++)
      |                     ~^~~~~~~~~~~~~~
dfam.cpp:239:25: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  504 |             for (int c=0; c<klist[k]->person.size(); c++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~~
dfam.cpp:151:11: warning: unused variable ‘totalInformative’ [-Wunused-variable]
  151 |       int totalInformative = 0;
      |           ^~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
fisher.cpp: In function ‘void fexact(int*, int*, double*, int*, double*, double*, double*, double*, double*, int*)’:
fisher.cpp:261:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  261 |       prterr(1, "NROW must be less than or equal to LDTABL.");
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fisher.cpp:267:21: 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.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
linput.cpp: In member function ‘void Plink::readDataLongFormat()’:
linput.cpp:68:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |       for (int l=0; l< locus.size(); l++)
      |                     ~^~~~~~~~~~~~~~
linput.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |       for (int i=0; i<sample.size(); i++)
      |                     ~^~~~~~~~~~~~~~
linput.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |       for (int l=0; l<SNP.size(); l++)
      |                     ~^~~~~~~~~~~
linput.cpp:146:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  146 |       for (int l=0; l< locus.size(); l++)
      |                     ~^~~~~~~~~~~~~~
linput.cpp:164:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  164 |               for (int i=0; i<sample.size(); i++)
      |                             ~^~~~~~~~~~~~~~
linput.cpp:200:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  200 |   for (int i=0; i<include.size(); i++)
      |                 ~^~~~~~~~~~~~~~~
linput.cpp:209:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  209 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
sockets.cpp: In function ‘std::vector<std::__cxx11::basic_string<char> > socketConnection(Plink*, std::string, int, std::string)’:
sockets.cpp:78:24: warning: unused variable ‘out_buf’ [-Wunused-variable]
   78 |   char                 out_buf[BUF_SIZE+1];  // Output buffer for GET request
      |                        ^~~~~~~
sockets.cpp:79:24: warning: unused variable ‘in_buf’ [-Wunused-variable]
   79 |   char                 in_buf[BUF_SIZE+1];   // Input buffer for response
      |                        ^~~~~~
sockets.cpp:81:24: warning: unused variable ‘i’ [-Wunused-variable]
   81 |   unsigned int         i;                    // Loop counter
      |                        ^
sockets.cpp:119:7: warning: unused variable ‘echoStringLen’ [-Wunused-variable]
  119 |   int echoStringLen = 100;
      |       ^~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
lookup.cpp: In member function ‘void Plink::lookup()’:
lookup.cpp:206:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  206 |             for (int i=25; i<tokens.size()-1; i++)
      |                            ~^~~~~~~~~~~~~~~~
lookup.cpp:203:15: 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  289 |           for (int i=25; i<tokens.size()-1; i++)
      |                          ~^~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from proxy.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
proxy.cpp: In member function ‘void Plink::performProxyTests(int)’:
proxy.cpp:314:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  314 |       for (int i=1; i<proxyHaplotypePlusSNP.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:332:29: warning: comparison of integer expressions of different signedness: ‘std::set<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  332 |           if ( added.size() >= par::proxy_snp_filter )
      |                ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:854:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  854 |           for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++)
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:1332:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1332 |           for (int l0=0; l0< proxyHaplotypePlusSNP.size(); l0++)
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proxy.cpp:1401:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1401 |       for (int c1 = 0; c1 < collection.size() ; c1++ )
      |                        ~~~^~~~~~~~~~~~~~~~~~~
proxy.cpp:1448:19: 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];
      |          ^
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from options.h:18:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator<int>]’,
    inlined from ‘void Plink::performProxyTests(int)’ at proxy.cpp:932:43:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘ref’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
proxy.cpp: In member function ‘void Plink::performProxyTests(int)’:
proxy.cpp:422:7: note: ‘ref’ was declared here
  422 |   int ref;
      |       ^~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from pdriver.cpp:18:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
pdriver.cpp: In member function ‘void Plink::proxyWrapper()’:
pdriver.cpp:266:11: warning: unused variable ‘similar’ [-Wunused-variable]
  266 |       int similar = 0;
      |           ^~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from haploQTL.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
haploQTL.cpp: In member function ‘void HaploPhase::haplotypicQTL(std::map<int, int>&, int, bool)’:
haploQTL.cpp:83:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   83 |           for (int z = 0 ; z < hap1[i].size(); z++)
      |                            ~~^~~~~~~~~~~~~~~~
haploQTL.cpp:145:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  145 |           for (int z = 0 ; z < hap1[i].size(); z++)
      |                            ~~^~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from haplohelper.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
In file included from haplohelper.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::imputeAllHaplotypes()’:
haplohelper.cpp:104:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |       for (int l=0; l<new_one[i].size(); l++)
      |                     ~^~~~~~~~~~~~~~~~~~
haplohelper.cpp:134:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  134 |   for (int l=0; l < actual_map.size(); l++)
      |                 ~~^~~~~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > HaploPhase::returnHaplotypes(std::vector<int>&)’:
haplohelper.cpp:297:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  297 |   for (int h=0; h<hap.size(); h++)
      |                 ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::setTestHaplotype(std::string)’:
haplohelper.cpp:337:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  337 |   for (int h=0; h<hap.size(); h++)
      |                 ~^~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhase()’:
haplohelper.cpp:396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  396 |           for (int z = 0; z < hap1[i].size(); z++)
      |                           ~~^~~~~~~~~~~~~~~~
haplohelper.cpp:413:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  413 |                   for (int z2=0; z2<hap1[i].size(); z2++)
      |                                  ~~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::reportPhaseWideFormat()’:
haplohelper.cpp:487:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  487 |           for (int z = 0; z < hap1[i].size(); z++)
      |                           ~~^~~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘vector_t HaploPhase::imputeGenotype(int, int)’:
haplohelper.cpp:655:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  655 |   for (int z=0; z<hap1[i].size(); z++)
      |                 ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::imputeHaplotypes(int, bool&, bool&)’:
haplohelper.cpp:754:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  754 |       for (int z=0; z<hap1[i].size(); z++)
      |                     ~^~~~~~~~~~~~~~~
haplohelper.cpp:802:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  802 |           for (int z=0; z<hap1[i].size(); z++)
      |                         ~^~~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘double HaploPhase::rsq_internal(boolvec_t&, boolvec_t&, boolvec_t&, boolvec_t&)’:
haplohelper.cpp:850:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |       ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:41: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |                            ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:850:65: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  850 |   if (mask1.size() != ns ||mask2.size() != ns ||alleles1.size() != ns
      |                                                 ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp:851:25: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  851 |       ||alleles2.size() != ns )
      |         ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘double HaploPhase::freq(boolvec_t&, boolvec_t&)’:
haplohelper.cpp:957:20: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  957 |   if (mask1.size() != ns ||alleles1.size() != ns )
      |       ~~~~~~~~~~~~~^~~~~
haplohelper.cpp:957:44: warning: comparison of integer expressions of different signedness: ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  957 |   if (mask1.size() != ns ||alleles1.size() != ns )
      |                            ~~~~~~~~~~~~~~~~^~~~~
haplohelper.cpp: In member function ‘void HaploPhase::trackThisSegment()’:
haplohelper.cpp:1225:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1225 |       for (int z = 0; z < hap1[p1].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1251:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1251 |       for (int z1 = 0; z1 < hap1[p1].size(); z1++)
      |                        ~~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1252:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1252 |         for (int z2 = 0; z2 < hap1[p2].size(); z2++)
      |                          ~~~^~~~~~~~~~~~~~~~~
haplohelper.cpp:1250:11: warning: unused variable ‘j’ [-Wunused-variable]
 1250 |       int j=0;
      |           ^
haplohelper.cpp: In member function ‘void HaploPhase::calculateEmpiricalVariance(std::set<int>&)’:
haplohelper.cpp:1419:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1419 |                 for( int z = 0; z < pp[i].size(); z++ )
      |                                 ~~^~~~~~~~~~~~~~
haplohelper.cpp:1477:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1477 |                   for( int z = 0; z < pp[i].size(); z++ )
      |                                   ~~^~~~~~~~~~~~~~
haplohelper.cpp: In member function ‘void HaploPhase::verboseDisplayWindows(int, bool)’:
haplohelper.cpp:1666:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1666 |       for (int z = 0; z < windows[w]->hap1[r].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from haplowindow.cpp:27:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
In file included from haplowindow.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
haplowindow.cpp: In function ‘void verboseDisplayWindows2(HaploPhase*, int, bool)’:
haplowindow.cpp:48:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |       for (int z = 0; z < haplo->windows[w]->hap1[r].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::enumerateHaplotypes(intvec_t&)’:
haplowindow.cpp:183:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  183 |   while (h<nh)
      |          ~^~~
haplowindow.cpp: In member function ‘void HaploWindow::prunePhase(int, double)’:
haplowindow.cpp:558:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  558 |   for (int z=0; z < hap1[i].size(); z++)
      |                 ~~^~~~~~~~~~~~~~~~
haplowindow.cpp:574:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  574 |       for (int z=0; z < new_pp.size(); z++)
      |                     ~~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::performEM()’:
haplowindow.cpp:683:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  683 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
haplowindow.cpp:691:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  691 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
haplowindow.cpp:751:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  751 |               for (int z=0; z<hap1[i].size(); z++)
      |                             ~^~~~~~~~~~~~~~~
haplowindow.cpp:791:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  791 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
haplowindow.cpp:798:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  798 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
haplowindow.cpp:868:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  868 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
haplowindow.cpp:872:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  872 |                 for (int z=0; z<hap1[i].size(); z++)
      |                               ~^~~~~~~~~~~~~~~
haplowindow.cpp: In member function ‘void HaploWindow::reportPhase()’:
haplowindow.cpp:949:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  949 |           for (int z = 0; z < hap1[i].size(); z++)
      |                           ~~^~~~~~~~~~~~~~~~
haplowindow.cpp:966:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  966 |                   for (int z2=0; z2<hap1[i].size(); z2++)
      |                                  ~~^~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from genogroup.cpp:24:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
In file included from genogroup.cpp:28:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from nonfounderphasing.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from nonfounderphasing.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::phaseAndScoreNonfounder(int)’:
nonfounderphasing.cpp:668:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  668 |     for (int z=0; z < pp[i].size(); z++)
      |                   ~~^~~~~~~~~~~~~~
nonfounderphasing.cpp:360:7: warning: unused variable ‘pcnt’ [-Wunused-variable]
  360 |   int pcnt=1;
      |       ^~~~
nonfounderphasing.cpp: In member function ‘void HaploPhase::transmissionCount(int, std::map<FamilyTransmissions, double>&)’:
nonfounderphasing.cpp:715:14: warning: unused variable ‘posterior’ [-Wunused-variable]
  715 |       double posterior = ip->second;
      |              ^~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from clumpld.cpp:21:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
clumpld.cpp: In member function ‘std::vector<ResultTrio> clump_LD::read_assoc_file(std::string)’:
clumpld.cpp:92:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   92 |   for (int f=0; f<filename.size(); f++)
      |                 ~^~~~~~~~~~~~~~~~
clumpld.cpp:128:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |       for (int i=0; i<tokens.size(); i++)
      |                     ~^~~~~~~~~~~~~~
clumpld.cpp:137:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  137 |             for ( int f=0; f<tok_annot.size(); f++)
      |                            ~^~~~~~~~~~~~~~~~~
clumpld.cpp:173:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  204 |                   if ( f < annot_field.size() - 1 )
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
clumpld.cpp: In member function ‘void clump_LD::clump()’:
clumpld.cpp:368:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResultTrio>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  368 |   for (int i = 0; i < sp.size(); i++)
      |                   ~~^~~~~~~~~~~
clumpld.cpp:480:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  480 |           if( l1 < P->locus.size()-1 )
      |               ~~~^~~~~~~~~~~~~~~~~~~
clumpld.cpp:520:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  520 |                   for (int f=1; f<=filename.size(); f++)
      |                                 ~^~~~~~~~~~~~~~~~~
clumpld.cpp:611:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  611 |                   for (int f=1; f<=filename.size(); f++)
      |                                 ~^~~~~~~~~~~~~~~~~
clumpld.cpp:1097:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int2, double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1097 |               if( j < grouped_snps.size()-1)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from genoerr.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from genoerr.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
genoerr.cpp: In member function ‘void HaploPhase::queryThisGenotype(int, int, int, vector_t&)’:
genoerr.cpp:157:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  157 |   for (int z=0; z<hap1[i].size(); z++)
      |                 ~^~~~~~~~~~~~~~~
genoerr.cpp:189:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  189 |       for( int a = 0; a < posshap1.size(); a++ )
      |                       ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:190:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  190 |         for( int b = 0; b < posshap2.size(); b++ )
      |                         ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:225:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  225 |   for (int z = 0; z < new_hap1.size(); z++)
      |                   ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:315:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  315 |       for (int z = 0; z < hap1[i].size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~
genoerr.cpp:328:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  328 |               for (int z2=0; z2<hap1[i].size(); z2++)
      |                              ~~^~~~~~~~~~~~~~~
genoerr.cpp:347:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  347 |       for (int z = 0; z < new_hap1.size(); z++)
      |                       ~~^~~~~~~~~~~~~~~~~
genoerr.cpp:358:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  358 |           for (int z2=0; z2<new_hap1.size(); z2++)
      |                          ~~^~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from em.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from em.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
em.cpp: In member function ‘void HaploPhase::performEM_original()’:
em.cpp:89:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   89 |                       for (int z=0; z<hap1[i].size(); z++)
      |                                     ~^~~~~~~~~~~~~~~
em.cpp:97:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   97 |                       for (int z=0; z<hap1[i].size(); z++)
      |                                     ~^~~~~~~~~~~~~~~
em.cpp:106:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  106 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
em.cpp:128:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |                   for (int z=0; z<hap1[i].size(); z++)
      |                                 ~^~~~~~~~~~~~~~~
em.cpp:132:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  132 |                 for (int z=0; z<hap1[i].size(); z++)
      |                               ~^~~~~~~~~~~~~~~
em.cpp:162:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  162 |                       for (int z=0; z<hap1[i].size(); z++)
      |                                     ~^~~~~~~~~~~~~~~
em.cpp:166:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |                     for (int z=0; z<hap1[i].size(); z++)
      |                                   ~^~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from impute.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from impute.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
impute.cpp: In constructor ‘probabilisticGenotype::probabilisticGenotype()’:
impute.cpp:40:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   40 |     phased = genotype = false;
      |              ~~~~~~~~~^~~~~~~
impute.cpp: In member function ‘void HaploPhase::updateForImputation()’:
impute.cpp:105:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |           for (int z=0; z<hap1[i].size(); z++)
      |                         ~^~~~~~~~~~~~~~~
impute.cpp:144:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |               for (int z=0; z< currentWindow->hap1[i].size(); z++)
      |                             ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp:161:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |               for (int z=0; z< currentWindow->pp[i].size(); z++)
      |                             ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp: In member function ‘void HaploPhase::mainImputation()’:
impute.cpp:263:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  263 |           for ( int z = 0 ; z < currentWindow->hap1[i].size(); z++)
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
impute.cpp:313:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<probabilisticGenotype>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  313 |       for (int s=0; s < g.size(); s++)
      |                     ~~^~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from metaem.cpp:27:
genogroup.h: In member function ‘bool MultiLocusGenotype::operator<(const MultiLocusGenotype&) const’:
genogroup.h:27:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
genogroup.h: In member function ‘bool MultiLocusGenotype::operator==(const MultiLocusGenotype&) const’:
genogroup.h:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     for (int i=0; i<g.size(); i++)
      |                   ~^~~~~~~~~
In file included from metaem.cpp:28:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
metaem.cpp: In member function ‘void HaploPhase::enumeratePhasedWindows(int)’:
metaem.cpp:239:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  239 |           while (h<nperm)
      |                  ~^~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::scoreIndividuals()’:
profile.cpp:303:12: warning: unused variable ‘OLD_assoc_glm_without_main_snp’ [-Wunused-variable]
  303 |       bool OLD_assoc_glm_without_main_snp = par::assoc_glm_without_main_snp;
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
profile.cpp:304:12: warning: unused variable ‘OLD_clist’ [-Wunused-variable]
  304 |       bool OLD_clist = par::clist;
      |            ^~~~~~~~~
profile.cpp:350:14: warning: unused variable ‘statistic’ [-Wunused-variable]
  350 |       double statistic = valid ? model->getStatistic() : 0;
      |              ^~~~~~~~~
profile.cpp:351:14: warning: unused variable ‘pvalue’ [-Wunused-variable]
  351 |       double pvalue = pval[ pval.size()-1 ];
      |              ^~~~~~
profile.cpp:352:14: warning: unused variable ‘beta’ [-Wunused-variable]
  352 |       double beta = b[ b.size()-1 ];
      |              ^~~~
profile.cpp:390:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  390 |       for (int s=0; s<snpset.size(); s++)
      |                     ~^~~~~~~~~~~~~~
profile.cpp:402:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  402 |           for (int s=0; s<snpset.size(); s++)
      |                         ~^~~~~~~~~~~~~~
profile.cpp:421:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  421 |   if ( qcnt == qlabel.size() )
      |        ~~~~~^~~~~~~~~~~~~~~~
profile.cpp: In member function ‘void Plink::calculateProfile(std::map<int, double>&, std::map<int, bool>&, vector_t&, matrix_t&, std::vector<int>&, std::vector<int>&)’:
profile.cpp:480:16: 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 ‘long unsigned int’} [-Wsign-compare]
  629 |           for (int j=0; j<snpset.size(); j++)
      |                         ~^~~~~~~~~~~~~~
profile.cpp: In function ‘void scoreRanges(int, std::vector<int>&, std::map<int, std::set<Range*> >&, std::map<Range*, int>&, std::ofstream&)’:
profile.cpp:667:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  667 |   for (int l=0; l<f.size(); l++)
      |                 ~^~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseNumberList(std::string)’:
nlist.cpp:38:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   38 |   for (int i=0; i<tok.size(); i++)
      |                 ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::deparseStringList(std::string, std::map<std::__cxx11::basic_string<char>, int>*)’:
nlist.cpp:83:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   83 |   for (int i=0; i<tok.size(); i++)
      |                 ~^~~~~~~~~~~
nlist.cpp: In member function ‘std::vector<int> NList::expandNumberList(std::vector<int>&)’:
nlist.cpp:107:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  107 |   for (int i=0; i<nlist.size(); i++)
      |                 ~^~~~~~~~~~~~~
nlist.cpp:124:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  124 |   for (int i=0; i<nlist.size(); i++)
      |                 ~^~~~~~~~~~~~~
nlist.cpp:151:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  151 |   for (int i=0; i<n.size(); i++)
      |                 ~^~~~~~~~~
nlist.cpp:160:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  160 |       for (int i=0; i<n.size(); i++)
      |                     ~^~~~~~~~~
nlist.cpp: In member function ‘std::vector<std::__cxx11::basic_string<char> > NList::tokenize(std::string)’:
nlist.cpp:189:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  189 |   for (int i=0; i<s.length(); i++)
      |                 ~^~~~~~~~~~~
nlist.cpp:239:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  239 |           if ( s[i]== range_char && i == s.length()-1 )
      |                                     ~~^~~~~~~~~~~~~~~
nlist.cpp:253:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  253 |       else if ( i == s.length()-1 )
      |                 ~~^~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from whap.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
whap.cpp: In member function ‘vector_t Plink::conditionalHaplotypeTest(bool, Perm&)’:
whap.cpp:334:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  334 |       for (int g = 0; g < nullModel.group.size(); g++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:393:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  393 |               for (int g=0; g<subnullModel.group.size(); g++)
      |                             ~^~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:454:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  454 |       for (int h=0; h<coeff1.size(); h++)
      |                     ~^~~~~~~~~~~~~~
whap.cpp:456:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  456 |       for (int h=0; h<coeff0.size(); h++)
      |                     ~^~~~~~~~~~~~~~
whap.cpp:508:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  508 |   for ( int g=0; g<nullModel.group.size(); g++ )
      |                  ~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:511:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  511 |       for ( int g2=0; g2<alternateModel.group.size(); g2++ )
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:619:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  619 |       if ( g < nullModel.group.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:670:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |       for (int s=0; s < conditioner.size(); s++)
      |                     ~~^~~~~~~~~~~~~~~~~~~~
whap.cpp:793:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  793 |    if ( p1 != coeff1.size() || p0 != coeff0.size() )
      |         ~~~^~~~~~~~~~~~~~~~
whap.cpp:793:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  793 |    if ( p1 != coeff1.size() || p0 != coeff0.size() )
      |                                ~~~^~~~~~~~~~~~~~~~
whap.cpp: In member function ‘void Chap::build(ChapModel&)’:
whap.cpp:962:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  962 |       for (int h=0; h<tok.size(); h++)
      |                     ~^~~~~~~~~~~
whap.cpp:986:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  986 |       for (int i=0; i<tok.size(); i++)
      |                     ~^~~~~~~~~~~
whap.cpp:1015:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1015 |               for (int i=0; i< tok.size(); i++)
      |                             ~^~~~~~~~~~~~
whap.cpp:1048:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1048 |       for ( int i = 0 ; i < tok.size() ; i++ )
      |                         ~~^~~~~~~~~~~~
whap.cpp:1118:27: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1118 |       if ( mapping.size() != H->ns + H->nh )
      |            ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
whap.cpp:1129:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1129 |       for (int i=0; i< lst.size(); i++)
      |                     ~^~~~~~~~~~~~
whap.cpp:1142:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1142 |           for (int i=0; i<lst.size(); i++)
      |                         ~^~~~~~~~~~~
whap.cpp:1162:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1162 |               for (int i=0; i<lst.size(); i++)
      |                             ~^~~~~~~~~~~
whap.cpp:1197:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1197 |       for (int i=0; i<snplist.size(); i++)
      |                     ~^~~~~~~~~~~~~~~
whap.cpp:1231:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1231 |           for (int i=0; i<lst.size(); i++)
      |                         ~^~~~~~~~~~~
whap.cpp:1290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1290 |   for (int g=0; g< model.group.size(); g++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
whap.cpp:1326:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1326 |       for (int c=0; c < P->conditioner.size(); c++)
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~
whap.cpp:1334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1334 |       for (int l=0; l<lst.size(); l++)
      |                     ~^~~~~~~~~~~
whap.cpp: In member function ‘void Chap::setSNPList(std::vector<int>&, ChapModel&)’:
whap.cpp:1389:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1389 |   for (int l=0;l<snplist.size(); l++)
      |                ~^~~~~~~~~~~~~~~
whap.cpp: In function ‘void displayHaploGroups(std::ofstream&, ChapModel&, HaploPhase*)’:
whap.cpp:1425:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1425 |   for (int h=0; h < m.group.size(); h++)
      |                 ~~^~~~~~~~~~~~~~~~
whap.cpp:1434:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::set<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1434 |           if ( cnt>0 && cnt2 < m.group[h].size() )
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
simul.cpp: In function ‘vector_t instanceSNP(SimParameters&)’:
simul.cpp:172:10: warning: unused variable ‘gh_11_12’ [-Wunused-variable]
  172 |   double gh_11_12 = h11*h12;
      |          ^~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs()’:
simul.cpp:635:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  635 |   for (int s=0; s<sp.size(); s++)
      |                 ~^~~~~~~~~~
simul.cpp:679:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParameters>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  679 |   for (int s=0; s<sp.size(); s++)
      |                 ~^~~~~~~~~~
simul.cpp: In member function ‘void Plink::simulateSNPs_QT()’:
simul.cpp:1146:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1146 |   for (int s=0; s<sp.size(); s++)
      |                 ~^~~~~~~~~~
simul.cpp:1211:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimParametersQT>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1211 |   for (int s=0; s<sp.size(); s++)
      |                 ~^~~~~~~~~~
simul.cpp:1358:30: warning: unused variable ‘cumU’ [-Wunused-variable]
 1358 |             double cumA = 0, cumU = 0;
      |                              ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
gvar.cpp: In member function ‘void Plink::readGenericVariantData()’:
gvar.cpp:125:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  125 |       for (int l=0; l<locus.size(); l++)
      |                     ~^~~~~~~~~~~~~
gvar.cpp:192:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  192 |       for (int l=0; l<locus.size(); l++)
      |                     ~^~~~~~~~~~~~~
gvar.cpp:247:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  247 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
gvar.cpp:298:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  298 |           for (int i=0; i<sample.size(); i++)
      |                         ~^~~~~~~~~~~~~~
gvar.cpp:381:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  381 |       for (int i=0; i<include.size(); i++)
      |                     ~^~~~~~~~~~~~~~~
gvar.cpp:395:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |       for (int i=0; i<include.size(); i++)
      |                     ~^~~~~~~~~~~~~~~
gvar.cpp:403:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  403 |   for (int i=0; i<sample.size(); i++)
      |                 ~^~~~~~~~~~~~~~
gvar.cpp:471:11: warning: unused variable ‘ip’ [-Wunused-variable]
  471 |       int ip = peri->second;
      |           ^~
gvar.cpp:414:8: warning: unused variable ‘fatal’ [-Wunused-variable]
  414 |   bool fatal = false;
      |        ^~~~~
gvar.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Locus*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  549 |       for (int l=0; l<locus.size(); l++)
      |                     ~^~~~~~~~~~~~~
gvar.cpp:553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CSNP*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  553 |         for (int l=0; l<SNP.size(); l++)
      |                       ~^~~~~~~~~~~
gvar.cpp:556:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  556 |         for (int i=0; i<sample.size(); i++)
      |                       ~^~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘void Plink::readCNVList()’:
cnv.cpp:247:15: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 2013 |   for (int c = 0 ; c < scaffold.size(); c++)
      |                    ~~^~~~~~~~~~~~~~~~~
cnv.cpp: In member function ‘vector_t Plink::glmCNVBurdenModel(Perm&, bool)’:
cnv.cpp:2098:13: warning: statement has no effect [-Wunused-value]
 2098 |     noCovar == true;
      |     ~~~~~~~~^~~~~~~
cnv.cpp:2202:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
 2202 |       indivPair p = ic->first;
      |                 ^
cnv.cpp:2288:10: warning: unused variable ‘statistic’ [-Wunused-variable]
 2288 |   double statistic = valid ? model->getStatistic() : 0;
      |          ^~~~~~~~~
cnv.cpp:2289:10: warning: unused variable ‘pvalue’ [-Wunused-variable]
 2289 |   double pvalue = pval[ pval.size()-1 ];
      |          ^~~~~~
cnv.cpp:2290:10: warning: unused variable ‘beta’ [-Wunused-variable]
 2290 |   double beta = b[ b.size()-1 ];
      |          ^~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
greport.cpp: In member function ‘void Plink::displayGeneReport()’:
greport.cpp:78:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
greport.cpp:147:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  147 |       if ( tokens.size() <= chr_column ||
      |            ~~~~~~~~~~~~~~^~~~~~~~~~~~~
greport.cpp:148:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  240 |               for (int l=0; l< ari->second.size(); l+=2)
      |                             ~^~~~~~~~~~~~~~~~~~~~
greport.cpp:125:7: warning: unused variable ‘cnt’ [-Wunused-variable]
  125 |   int cnt = 0;
      |       ^~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
qualscores.cpp: In member function ‘void Plink::filterQualGenotypes()’:
qualscores.cpp:122:12: warning: unused variable ‘nfound’ [-Wunused-variable]
  122 |   long int nfound = 0;
      |            ^~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
cfamily.cpp: In function ‘int mCount(Individual*, Individual*)’:
cfamily.cpp:205:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  205 |       for (int i = 0 ; i < inds.size() ; i++)
      |                        ~~^~~~~~~~~~~~~
cfamily.cpp:221:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |               for (int j = 0 ; j < inds[i]->kids.size() ; j++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:237:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |        for (int i = 0 ; i < inds.size() ; i++)
      |                         ~~^~~~~~~~~~~~~
cfamily.cpp: In function ‘bool isAncestorOf(Individual*, Individual*)’:
cfamily.cpp:263:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  263 |       for (int i = 0 ; i < inds.size() ; i++)
      |                        ~~^~~~~~~~~~~~~
cfamily.cpp:276:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  276 |               for (int j = 0 ; j < inds[i]->kids.size() ; j++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~
cfamily.cpp:288:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  288 |       for (int i = 0 ; i < inds.size() ; i++)
      |                        ~~^~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
setscreen.cpp: In member function ‘void Plink::setAssocSummary()’:
setscreen.cpp:80:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   80 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
setscreen.cpp:110:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  110 |       if ( tokens.size() != cols )
      |            ~~~~~~~~~~~~~~^~~~~~~
setscreen.cpp:188:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |   for ( int j = 0; j < pS->snpset.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
setscreen.cpp:196:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  196 |       for (int i=0; i < snpset[j].size(); i++)
      |                     ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
  196 |     for (int k=0; k<values.size(); k++)
      |                   ~^~~~~~~~~~~~~~
In file included from idhelp.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘std::map<IDField*, std::set<IDValue> > IDHelper::parseQuery(std::string)’:
idhelp.cpp:40:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |   for ( int i = 0 ; i < ids.size() ; i++)
      |                     ~~^~~~~~~~~~~~
idhelp.cpp:63:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   63 |           for (int i=0; i<flist.size(); i++)
      |                         ~^~~~~~~~~~~~~
idhelp.cpp: In member function ‘bool IDHelper::matchIndividual(IDGroup*, std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:136:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |   for (int g=0; g<group->values.size(); g++)
      |                 ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:169:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<IDField*, std::set<IDValue> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  169 |   if ( found != matchTemplate.size() )
      |        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:128:8: warning: unused variable ‘match’ [-Wunused-variable]
  128 |   bool match = true;
      |        ^~~~~
idhelp.cpp: In member function ‘void IDHelper::setJointValues(IDGroup*)’:
idhelp.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int j = 0 ; j < jointField.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:221:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:296:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  296 |           for ( int i = 0 ; i < mask.size() ; i++)
      |                             ~~^~~~~~~~~~~~~
idhelp.cpp:214:26: warning: unused variable ‘jo’ [-Wunused-variable]
  214 |       vector<IDField*> & jo = jointOrder[j];
      |                          ^~
idhelp.cpp: In member function ‘std::set<IDGroup*> IDHelper::findAllIndividuals(std::map<IDField*, std::set<IDValue> >&)’:
idhelp.cpp:346:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  346 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idHelp()’:
idhelp.cpp:502:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  502 |           if ( ++p == tokens.size() )
      |                ~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:510:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  510 |       if ( p < tokens.size() )
      |            ~~^~~~~~~~~~~~~~~
idhelp.cpp:542:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  542 |                   for (int i = 0 ; i < ids.size() ; i++)
      |                                    ~~^~~~~~~~~~~~
idhelp.cpp:547:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  547 |                   for (int i = 0 ; i < ids.size() ; i++)
      |                                    ~~^~~~~~~~~~~~
idhelp.cpp:553:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  553 |                   for (int i = 0 ; i < ids.size() ; i++)
      |                                    ~~^~~~~~~~~~~~
idhelp.cpp:529:24: 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  678 |               if ( ++p == tokens.size() )
      |                    ~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:727:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  727 |   for ( int f = 0 ; f < files.size() ; f++ )
      |                     ~~^~~~~~~~~~~~~~
idhelp.cpp:742:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  742 |   for (int j = 0 ; j < jointField.size(); j++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:745:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  745 |       for ( int f = 0 ; f < files.size() ; f++ )
      |                         ~~^~~~~~~~~~~~~~
idhelp.cpp:747:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  747 |           for ( int j = 0; j < files[f].fields.size(); j++)
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:757:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  757 |                       for ( int j = 0; j < files[f].fields.size(); j++)
      |                                        ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:744:23: warning: unused variable ‘jf’ [-Wunused-variable]
  744 |       set<IDField*> & jf = jointField[j];
      |                       ^~
idhelp.cpp:772:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<IDField*> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  772 |       for (int j = 0 ; j < jointField.size(); j++ )
      |                        ~~^~~~~~~~~~~~~~~~~~~
idhelp.cpp:790:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDFile>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  790 |   for ( int f = 0 ; f < files.size() ; f++ )
      |                     ~~^~~~~~~~~~~~~~
idhelp.cpp:794:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  794 |       for ( int j = 0 ; j < files[f].fields.size(); j++ )
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:808:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDField*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  808 |       for ( int j = 0 ; j < files[f].fields.size(); j++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:836:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  836 |                   for (int k = 0 ; k < i->second.size(); k++)
      |                                    ~~^~~~~~~~~~~~~~~~~~
idhelp.cpp:888:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  975 |                   if ( v->value.size() + 3 > myField->width )
      |                        ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
idhelp.cpp:1000:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1000 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1003:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1003 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1013:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1013 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1015:17: warning: unused variable ‘group’ [-Wunused-variable]
 1015 |       IDGroup * group = idgroup[g];
      |                 ^~~~~
idhelp.cpp:1025:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1025 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1028:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1028 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1031:21: 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1189 |                               for (int z=0; z<(*i0)->values.size(); z++)
      |                                             ~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1236:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1236 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1242:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1242 |       for (int j = 0 ; j < group->values.size(); j++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1245:21: 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 ‘long unsigned int’} [-Wsign-compare]
 1346 |       for (int i=0; i<ids.size(); i++)
      |                     ~^~~~~~~~~~~
idhelp.cpp:1424:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1424 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:1440:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1440 |       for ( int j = 0; j < group->values.size(); j++ )
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idReplace()’:
idhelp.cpp:1551:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1551 |   for ( int i=0; i<targetFields.size(); i++)
      |                  ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1631 |       for (int i=0; i<ids.size(); i++)
      |                     ~^~~~~~~~~~~
idhelp.cpp:1648:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1648 |       for (int f = 0 ; f < targetFields.size(); f++)
      |                        ~~^~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1649:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1649 |         for (int i = 0 ; i < tokens.size(); i++)
      |                          ~~^~~~~~~~~~~~~~~
idhelp.cpp:1654:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1654 |       for (int i=0; i<rep_field.size(); i++)
      |                     ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1675:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1675 |   for (int i=0; i<rep_field.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1684:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1684 |       if ( tokens.size() <= maxfield )
      |            ~~~~~~~~~~~~~~^~~~~~~~~~~
idhelp.cpp:1692:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1692 |           for (int i=0; i<rep_field.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1710:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1710 |           for (int i=0; i<rep_field.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1733:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1784 |               for (int f=0; f<targetFields.size(); f++)
      |                             ~^~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1801:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1801 |       for (int i = 0 ; i < tokens.size() ; i++ )
      |                        ~~^~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idMatch()’:
idhelp.cpp:1856:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1856 |   for (int s=0; s< par::idhelp_match_string.size(); s+=2)
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
idhelp.cpp:1903:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 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 ‘long 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 ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
 2018 |             if ( tok.size() != tableSize[t] )
idhelp.cpp:2024:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2024 |                 for (int k=0; k<tok.size(); k++)
      |                               ~^~~~~~~~~~~
idhelp.cpp:2030:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 2070 |                   for (int v=0; v<g->values.size(); v++)
      |                                 ~^~~~~~~~~~~~~~~~~
idhelp.cpp:1889:12: warning: unused variable ‘jointQuery’ [-Wunused-variable]
 1889 |       bool jointQuery = id.find("+") != string::npos;
      |            ^~~~~~~~~~
idhelp.cpp:2167:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2167 |       for (int k=0; k<headers.size(); k++)
      |                     ~^~~~~~~~~~~~~~~
idhelp.cpp:2168:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 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 ‘long unsigned int’} [-Wsign-compare]
 2201 |               for (int k = 0 ; k < thisLine.size() ; k++ )
      |                                ~~^~~~~~~~~~~~~~~~~
idhelp.cpp: In member function ‘void IDHelper::idDump()’:
idhelp.cpp:2229:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDGroup*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2229 |   for ( int g = 0 ; g < idgroup.size(); g++ )
      |                     ~~^~~~~~~~~~~~~~~~
idhelp.cpp:2234:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2234 |           for (int j = 0 ; j < group->values.size(); j++ )
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from hapglm.cpp:25:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
lookup2.cpp: In member function ‘void Plink::lookup2()’:
lookup2.cpp:163:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:203:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  203 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:280:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  280 |        for (int i = 0 ; i < ids.size(); i++)
      |                         ~~^~~~~~~~~~~~
lookup2.cpp:325:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  325 |    for (int t = 0 ; t < tokens.size() ; t++)
      |                     ~~^~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from blox.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
blox.cpp: In member function ‘std::map<Range, std::vector<int> > Plink::mkBlks(int, int)’:
blox.cpp:147:11: warning: unused variable ‘nsnps’ [-Wunused-variable]
  147 |       int nsnps = toPosition - fromPosition + 1;
      |           ^~~~~
blox.cpp:156:11: warning: unused variable ‘numStrong’ [-Wunused-variable]
  156 |       int numStrong = 0;
      |           ^~~~~~~~~
blox.cpp:157:11: warning: unused variable ‘numRec’ [-Wunused-variable]
  157 |       int numRec = 0;
      |           ^~~~~~
blox.cpp:158:11: warning: unused variable ‘numInGroup’ [-Wunused-variable]
  158 |       int numInGroup = 0;
      |           ^~~~~~~~~~
blox.cpp:226:11: warning: unused variable ‘cnt’ [-Wunused-variable]
  226 |       int cnt = 0;
      |           ^~~
blox.cpp:418:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  418 |       for (int k=0; k<b.size(); k++)
      |                     ~^~~~~~~~~
blox.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  427 |       for (int k=0; k<b.size(); k++)
      |                     ~^~~~~~~~~
blox.cpp:123:16: warning: unused variable ‘fourGameteCutoff’ [-Wunused-variable]
  123 |   const double fourGameteCutoff = 0.01;
      |                ^~~~~~~~~~~~~~~~
blox.cpp: In member function ‘void PairwiseLinkage::calculateCI()’:
blox.cpp:469:7: warning: unused variable ‘total_chroms’ [-Wunused-variable]
  469 |   int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH;
      |       ^~~~~~~~~~~~
blox.cpp:569:41: warning: ‘pB2’ may be used uninitialized [-Wmaybe-uninitialized]
  569 |   if ( pB1>0 ) loglike1 += knownBA * log( pB1 );
      |                                      ~~~^~~~~~~
blox.cpp:489:22: note: ‘pB2’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |                      ^~~
blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized [-Wmaybe-uninitialized]
  505 |   double p1 = pA1 + pB1;
      |          ^~
blox.cpp:489:18: note: ‘pB1’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |                  ^~~
blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized [-Wmaybe-uninitialized]
  503 |   double pA = pA1 + pA2;
      |          ^~
blox.cpp:489:14: note: ‘pA2’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |              ^~~
blox.cpp:510:10: warning: ‘pA1’ may be used uninitialized [-Wmaybe-uninitialized]
  510 |   double D = pA1 - (pA*p1);
      |          ^
blox.cpp:489:10: note: ‘pA1’ was declared here
  489 |   double pA1,pA2,pB1,pB2;
      |          ^~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from dosage.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
dosage.cpp: In member function ‘void Plink::processDosageFile()’:
dosage.cpp:110:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double2>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  110 |               for ( int q = 0 ; q < qthresh.size() ; q++)
      |                                 ~~^~~~~~~~~~~~~~~~
dosage.cpp:513:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  513 |           for (int i=0; i<dosageFilename_all.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~
dosage.cpp:548:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ZInput*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       for (int f = 0 ; f < vzin.size() ; f++ )
      |                        ~~^~~~~~~~~~~~~
dosage.cpp:581:27: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  581 |           if ( tok.size() < firstCol )
      |                ~~~~~~~~~~~^~~~~~~~~~
dosage.cpp:601:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  601 |           for (int i=firstCol; i<tok.size(); i+= 2 )
      |                                ~^~~~~~~~~~~
dosage.cpp:695:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Individual*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  695 |           for (int i = 0; i < personMap[f].size(); i++)
      |                           ~~^~~~~~~~~~~~~~~~~~~~~
dosage.cpp:750:31: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  750 |               if ( tok.size() != expected[f] )
dosage.cpp:989:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  989 |                   for (int q=0; q<inQ.size(); q++)
      |                                 ~^~~~~~~~~~~
dosage.cpp:1170:18: 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1310 |           if ( ++qq == qthresh.size() )
      |                ~~~~~^~~~~~~~~~~~~~~~~
dosage.cpp:190:7: warning: unused variable ‘geno_field’ [-Wunused-variable]
  190 |   int geno_field = a2_field + skip2 + 1;
      |       ^~~~~~~~~~
In file included from /usr/mips64el-linux-gnuabi64/include/c++/12/vector:64,
                 from options.h:18:
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = CSNP*; _Alloc = std::allocator<CSNP*>]’,
    inlined from ‘void Plink::processDosageFile()’ at dosage.cpp:915:21:
/usr/mips64el-linux-gnuabi64/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘snp_code’ may be used uninitialized [-Wmaybe-uninitialized]
 1124 |         return *(this->_M_impl._M_start + __n);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
dosage.cpp: In member function ‘void Plink::processDosageFile()’:
dosage.cpp:725:15: note: ‘snp_code’ was declared here
  725 |           int snp_code;
      |               ^~~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
annot.cpp: In member function ‘void Plink::annotateFile()’:
annot.cpp:83:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   83 |           for (int j=1; j<tok.size(); j++)
      |                         ~^~~~~~~~~~~
annot.cpp:149:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  149 |   for (int i=0; i<tokens.size(); i++)
      |                 ~^~~~~~~~~~~~~~
annot.cpp:250:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  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 ‘long 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 ‘long 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 ‘long 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;
      |                ^~~~~~~
mips64el-linux-gnuabi64-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 ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
metaanal.cpp: In constructor ‘Alleles::Alleles(std::string, int, int, std::string, std::string)’:
metaanal.cpp:47:7: warning: ‘Alleles::bp’ will be initialized after [-Wreorder]
   47 |   int bp;
      |       ^~
metaanal.cpp:44:10: warning:   ‘std::string Alleles::a1’ [-Wreorder]
   44 |   string a1;
      |          ^~
metaanal.cpp:61:3: warning:   when initialized here [-Wreorder]
   61 |   Alleles(string name, int chr, int bp, string a1, string a2)
      |   ^~~~~~~
metaanal.cpp: In member function ‘void Plink::metaAnalysis()’:
metaanal.cpp:159:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  159 |       for (int f=0; f<ns.size(); f++)
      |                     ~^~~~~~~~~~
metaanal.cpp:182:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  182 |       for (int f=0; f<ns.size(); f++)
      |                     ~^~~~~~~~~~
metaanal.cpp:203:18: warning: statement has no effect [-Wunused-value]
  203 |     par::run_chr == -1;
      |     ~~~~~~~~~~~~~^~~~~
metaanal.cpp:213:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  213 |           for (int i=0; i<tok.size(); i++)
      |                         ~^~~~~~~~~~~
metaanal.cpp:235:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |   for (int f = 0 ; f < par::meta_files.size() ; f++ )
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:261:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  261 |       for (int i=0; i<tokens.size(); i++)
      |                     ~^~~~~~~~~~~~~~
metaanal.cpp:300:30: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  300 |           if ( tokens.size() != fsize )
      |                ~~~~~~~~~~~~~~^~~~~~~~
metaanal.cpp:253:11: warning: variable ‘pval_column’ set but not used [-Wunused-but-set-variable]
  253 |       int pval_column = -1;
      |           ^~~~~~~~~~~
metaanal.cpp:482:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  482 |     for (int f=0; f<par::meta_files.size(); f++)
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
metaanal.cpp:637:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  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 ‘long unsigned int’} [-Wsign-compare]
  680 |             for (int f=0; f<par::meta_files.size(); f++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~
mips64el-linux-gnuabi64-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 Rconnection.h:42,
                 from r.cpp:29:
Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp]
  327 |     #warning using little endian based on information from endian.h
      |      ^~~~~~~
In file included from helper.h:24,
                 from r.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
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 [-Wmaybe-uninitialized]
  380 |         delete rCov;
      |                ^~~~
r.cpp:165:13: note: ‘rCov’ was declared here
  165 |   Rdouble * rCov;
      |             ^~~~
r.cpp:378:14: warning: ‘rS’ may be used uninitialized [-Wmaybe-uninitialized]
  378 |       delete rS;
      |              ^~
r.cpp:164:14: note: ‘rS’ was declared here
  164 |   Rinteger * rS;
      |              ^~
r.cpp:377:14: warning: ‘rP’ may be used uninitialized [-Wmaybe-uninitialized]
  377 |       delete rP;
      |              ^~
r.cpp:163:13: note: ‘rP’ was declared here
  163 |   Rdouble * rP;
      |             ^~
r.cpp:376:14: warning: ‘rN’ may be used uninitialized [-Wmaybe-uninitialized]
  376 |       delete rN;
      |              ^~
r.cpp:162:14: note: ‘rN’ was declared here
  162 |   Rinteger * rN;
      |              ^~
r.cpp:399:10: warning: ‘rc’ may be used uninitialized [-Wmaybe-uninitialized]
  399 |   delete rc;
      |          ^~
r.cpp:68:16: note: ‘rc’ was declared here
   68 |   Rconnection *rc;
      |                ^~
mips64el-linux-gnuabi64-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.h:42,
                 from Rconnection.cpp:30:
Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp]
  327 |     #warning using little endian based on information from endian.h
      |      ^~~~~~~
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;
      |                           ^~~~
mips64el-linux-gnuabi64-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
mips64el-linux-gnuabi64-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_mips64el.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_mips64el.deb'.
 dpkg-genbuildinfo --build=any -O../plink_1.07+dfsg-4_mips64el.buildinfo
 dpkg-genchanges --build=any -O../plink_1.07+dfsg-4_mips64el.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 2023-04-17T01:32:59Z

Finished
--------

I: Built successfully

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


plink_1.07+dfsg-4_mips64el.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: mips64el
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"
Checksums-Sha1:
 5db314f12f75450c7453a9763e36967893313593 26988324 plink-dbgsym_1.07+dfsg-4_mips64el.deb
 b1ed214fe307d45eca85a56a5717a5f85ec12653 5327 plink_1.07+dfsg-4_mips64el.buildinfo
 e0dbaa03f315b51ec27344fa32f3128c8459df70 1053576 plink_1.07+dfsg-4_mips64el.deb
Checksums-Sha256:
 e5e77b31ddd7283ca484b18a8fd45cf4b2919b1b49739e0d12ff65964eeee82d 26988324 plink-dbgsym_1.07+dfsg-4_mips64el.deb
 1d47de56ac617b3f7ea35e5696570dc4b9e9e8790ce52ed4331e66dfb5b9ae07 5327 plink_1.07+dfsg-4_mips64el.buildinfo
 cf97ffe1f0ef754e1b8d15991e048e18c8b87d3d05e777759402061a1b486a56 1053576 plink_1.07+dfsg-4_mips64el.deb
Files:
 fa5730ba5b872f9fb65647fbb936c609 26988324 debug optional plink-dbgsym_1.07+dfsg-4_mips64el.deb
 b047abb1eb1041f37d3a6d44f396f973 5327 science optional plink_1.07+dfsg-4_mips64el.buildinfo
 daffffb5e6d08bb63e0fc45d9b861b33 1053576 science optional plink_1.07+dfsg-4_mips64el.deb
/<<BUILDDIR>>/plink_1.07+dfsg-4_mips64el.changes.new could not be renamed to /<<BUILDDIR>>/plink_1.07+dfsg-4_mips64el.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: plink
Binary: plink plink-dbgsym
Architecture: mips64el
Version: 1.07+dfsg-4
Checksums-Md5:
 fa5730ba5b872f9fb65647fbb936c609 26988324 plink-dbgsym_1.07+dfsg-4_mips64el.deb
 daffffb5e6d08bb63e0fc45d9b861b33 1053576 plink_1.07+dfsg-4_mips64el.deb
Checksums-Sha1:
 5db314f12f75450c7453a9763e36967893313593 26988324 plink-dbgsym_1.07+dfsg-4_mips64el.deb
 e0dbaa03f315b51ec27344fa32f3128c8459df70 1053576 plink_1.07+dfsg-4_mips64el.deb
Checksums-Sha256:
 e5e77b31ddd7283ca484b18a8fd45cf4b2919b1b49739e0d12ff65964eeee82d 26988324 plink-dbgsym_1.07+dfsg-4_mips64el.deb
 cf97ffe1f0ef754e1b8d15991e048e18c8b87d3d05e777759402061a1b486a56 1053576 plink_1.07+dfsg-4_mips64el.deb
Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Mon, 17 Apr 2023 01:32:58 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
Installed-Build-Depends:
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-12),
 autotools-dev (= 20220109.1),
 base-files (= 12.4),
 base-passwd (= 3.6.1),
 bash (= 5.2.15-2+b1),
 binutils (= 2.40-2),
 binutils-common (= 2.40-2),
 binutils-x86-64-linux-gnu (= 2.40-2),
 bsdextrautils (= 2.38.1-5+b1),
 bsdutils (= 1:2.38.1-5+b1),
 build-essential (= 12.9),
 bzip2 (= 1.0.8-5+b1),
 coreutils (= 9.1-1),
 cpp (= 4:12.2.0-3),
 cpp-11 (= 11.3.0-12),
 cpp-12 (= 12.2.0-14),
 dash (= 0.5.12-2),
 debconf (= 1.5.82),
 debhelper (= 13.11.4),
 debianutils (= 5.7-0.4),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.13.1-1),
 diffutils (= 1:3.8-4),
 dpkg (= 1.21.21),
 dpkg-dev (= 1.21.21),
 dwz (= 0.15-1),
 file (= 1:5.44-3),
 findutils (= 4.9.0-4),
 g++ (= 4:12.2.0-3),
 g++-12 (= 12.2.0-14),
 gcc (= 4:12.2.0-3),
 gcc-11 (= 11.3.0-12),
 gcc-11-base (= 11.3.0-12),
 gcc-12 (= 12.2.0-14),
 gcc-12-base (= 12.2.0-14),
 gettext (= 0.21-12),
 gettext-base (= 0.21-12),
 grep (= 3.8-5),
 groff-base (= 1.22.4-10),
 gzip (= 1.12-1),
 hostname (= 3.23+nmu1),
 init-system-helpers (= 1.65.2),
 intltool-debian (= 0.35.0+20060710.6),
 libacl1 (= 2.3.1-3),
 libarchive-zip-perl (= 1.68-1),
 libasan6 (= 11.3.0-12),
 libasan8 (= 12.2.0-14),
 libatomic1 (= 12.2.0-14),
 libattr1 (= 1:2.5.1-4),
 libaudit-common (= 1:3.0.9-1),
 libaudit1 (= 1:3.0.9-1),
 libbinutils (= 2.40-2),
 libblkid1 (= 2.38.1-5+b1),
 libbz2-1.0 (= 1.0.8-5+b1),
 libc-bin (= 2.36-9),
 libc-dev-bin (= 2.36-9),
 libc6 (= 2.36-9),
 libc6-dev (= 2.36-9),
 libcap-ng0 (= 0.8.3-1+b3),
 libcap2 (= 1:2.66-3),
 libcc1-0 (= 12.2.0-14),
 libcom-err2 (= 1.47.0-2),
 libcrypt-dev (= 1:4.4.33-2),
 libcrypt1 (= 1:4.4.33-2),
 libctf-nobfd0 (= 2.40-2),
 libctf0 (= 2.40-2),
 libdb5.3 (= 5.3.28+dfsg2-1),
 libdebconfclient0 (= 0.268),
 libdebhelper-perl (= 13.11.4),
 libdpkg-perl (= 1.21.21),
 libelf1 (= 0.188-2.1),
 libfile-find-rule-perl (= 0.34-3),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgcc-11-dev (= 11.3.0-12),
 libgcc-12-dev (= 12.2.0-14),
 libgcc-s1 (= 12.2.0-14),
 libgcrypt20 (= 1.10.1-3),
 libgdbm-compat4 (= 1.23-3),
 libgdbm6 (= 1.23-3),
 libgmp10 (= 2:6.2.1+dfsg1-1.1),
 libgomp1 (= 12.2.0-14),
 libgpg-error0 (= 1.46-1),
 libgprofng0 (= 2.40-2),
 libgssapi-krb5-2 (= 1.20.1-1+b1),
 libicu72 (= 72.1-3),
 libisl23 (= 0.25-1),
 libitm1 (= 12.2.0-14),
 libjansson4 (= 2.14-2),
 libk5crypto3 (= 1.20.1-1+b1),
 libkeyutils1 (= 1.6.3-2),
 libkrb5-3 (= 1.20.1-1+b1),
 libkrb5support0 (= 1.20.1-1+b1),
 liblsan0 (= 12.2.0-14),
 liblz4-1 (= 1.9.4-1),
 liblzma5 (= 5.4.1-0.2),
 libmagic-mgc (= 1:5.44-3),
 libmagic1 (= 1:5.44-3),
 libmd0 (= 1.0.4-2),
 libmount1 (= 2.38.1-5+b1),
 libmpc3 (= 1.3.1-1),
 libmpfr6 (= 4.2.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libnumber-compare-perl (= 0.03-3),
 libpam-modules (= 1.5.2-6),
 libpam-modules-bin (= 1.5.2-6),
 libpam-runtime (= 1.5.2-6),
 libpam0g (= 1.5.2-6),
 libpcre2-8-0 (= 10.42-1),
 libperl5.36 (= 5.36.0-7),
 libpipeline1 (= 1.5.7-1),
 libquadmath0 (= 12.2.0-14),
 libseccomp2 (= 2.5.4-1+b3),
 libselinux1 (= 3.4-1+b5),
 libsmartcols1 (= 2.38.1-5+b1),
 libssl3 (= 3.0.8-1),
 libstdc++-12-dev (= 12.2.0-14),
 libstdc++6 (= 12.2.0-14),
 libsub-override-perl (= 0.09-4),
 libsystemd0 (= 252.6-1),
 libtext-glob-perl (= 0.11-3),
 libtinfo6 (= 6.4-2),
 libtirpc-common (= 1.3.3+ds-1),
 libtirpc-dev (= 1.3.3+ds-1),
 libtirpc3 (= 1.3.3+ds-1),
 libtool (= 2.4.7-5),
 libtsan0 (= 11.3.0-12),
 libtsan2 (= 12.2.0-14),
 libubsan1 (= 12.2.0-14),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 252.6-1),
 libunistring2 (= 1.0-2),
 libuuid1 (= 2.38.1-5+b1),
 libxml2 (= 2.9.14+dfsg-1.1+b3),
 libzstd1 (= 1.5.4+dfsg2-5),
 linux-libc-dev (= 6.1.20-2),
 login (= 1:4.13+dfsg1-1+b1),
 m4 (= 1.4.19-3),
 make (= 4.3-4.1),
 man-db (= 2.11.2-2),
 mawk (= 1.3.4.20200120-3.1),
 ncurses-base (= 6.4-2),
 ncurses-bin (= 6.4-2),
 patch (= 2.7.6-7),
 perl (= 5.36.0-7),
 perl-base (= 5.36.0-7),
 perl-modules-5.36 (= 5.36.0-7),
 po-debconf (= 1.0.21+nmu1),
 rpcsvc-proto (= 1.4.3-1),
 sed (= 4.9-1),
 sensible-utils (= 0.0.17+nmu1),
 sysvinit-utils (= 3.06-4),
 tar (= 1.34+dfsg-1.2),
 usrmerge (= 35),
 util-linux (= 2.38.1-5+b1),
 util-linux-extra (= 2.38.1-5+b1),
 xz-utils (= 5.4.1-0.2),
 zlib1g (= 1:1.2.13.dfsg-1),
 zlib1g-dev (= 1:1.2.13.dfsg-1)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_US.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 SOURCE_DATE_EPOCH="1635694306"


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


plink-dbgsym_1.07+dfsg-4_mips64el.deb
-------------------------------------

 new Debian package, version 2.0.
 size 26988324 bytes: control archive=540 bytes.
     375 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: mips64el
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 26883
 Depends: plink (= 1.07+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for plink
 Build-Ids: 8da0c2ded6029a9bd527cee24aa2c4f35a4035d4

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/8d/
-rw-r--r-- root/root  27517568 2021-10-31 15:31 ./usr/lib/debug/.build-id/8d/a0c2ded6029a9bd527cee24aa2c4f35a4035d4.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_mips64el.deb
------------------------------

 new Debian package, version 2.0.
 size 1053576 bytes: control archive=1300 bytes.
    1097 bytes,    26 lines      control              
     915 bytes,    13 lines      md5sums              
 Package: plink
 Version: 1.07+dfsg-4
 Architecture: mips64el
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4179
 Depends: libc6 (>= 2.34), 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   4232064 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       720 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:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [540 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [629 B]
Fetched 2132 B in 0s (0 B/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:
  ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-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 libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl
  liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2
  libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl libreadline8
  libregexp-ipv6-perl libregexp-wildcards-perl 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-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 libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzop netbase openssl patchutils
  perl-openssl-defaults plzip readline-common t1utils unzip
Suggested packages:
  isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl
  libscalar-number-perl libbareword-filehandles-perl libindirect-perl
  libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl
  binutils-multiarch libtext-template-perl readline-doc zip
Recommended packages:
  gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl
  libfreezethaw-perl libmath-base85-perl libsocket6-perl
  libpackage-stash-xs-perl libxstring-perl libdata-dump-perl
  libhttp-daemon-perl libmailtools-perl
The following NEW packages will be installed:
  ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-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 libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl
  liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2
  libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl libreadline8
  libregexp-ipv6-perl libregexp-wildcards-perl 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-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 libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzop netbase openssl patchutils
  perl-openssl-defaults plzip readline-common
  sbuild-build-depends-lintian-dummy:mips64el t1utils unzip
0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded.
Need to get 13.7 MB of archives.
After this operation, 51.3 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://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB]
Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.8-1 [1407 kB]
Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB]
Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB]
Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB]
Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB]
Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB]
Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB]
Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.13.0-1 [2899 kB]
Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB]
Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB]
Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB]
Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB]
Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB]
Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB]
Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB]
Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get:28 http://localhost:3142/debian sid/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get:29 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.17-1 [90.4 kB]
Get:30 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB]
Get:31 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.55-1 [220 kB]
Get:32 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:33 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB]
Get:34 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB]
Get:35 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB]
Get:36 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-2 [16.4 kB]
Get:37 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB]
Get:38 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:39 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.113-1 [10.6 kB]
Get:40 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.989-1 [50.5 kB]
Get:41 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get:42 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.35-1 [131 kB]
Get:43 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get:44 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:45 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:46 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:47 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-2 [43.6 kB]
Get:48 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB]
Get:49 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB]
Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB]
Get:51 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:52 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:53 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB]
Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:55 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB]
Get:56 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB]
Get:57 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB]
Get:58 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:59 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:60 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:61 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:62 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB]
Get:63 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB]
Get:64 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:65 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:66 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:67 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB]
Get:68 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB]
Get:69 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:70 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:71 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB]
Get:72 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:73 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B]
Get:74 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB]
Get:75 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB]
Get:76 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB]
Get:77 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB]
Get:78 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:79 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.68-1 [186 kB]
Get:80 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:81 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:82 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-2 [11.0 kB]
Get:83 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB]
Get:84 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004004-1 [13.3 kB]
Get:85 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:86 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:87 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:88 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-5 [37.7 kB]
Get:89 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB]
Get:90 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB]
Get:91 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:92 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:93 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:94 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:95 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:96 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:97 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB]
Get:98 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:99 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB]
Get:100 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-2+b1 [12.6 kB]
Get:101 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:102 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB]
Get:103 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB]
Get:104 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB]
Get:105 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b2 [43.1 kB]
Get:106 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:107 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.003+ds-1 [99.5 kB]
Get:108 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.003+ds-1 [102 kB]
Get:109 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B]
Get:110 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.33-1 [58.4 kB]
Get:111 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.28-1 [28.6 kB]
Get:112 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB]
Get:113 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B]
Get:114 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB]
Get:115 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB]
Get:116 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:117 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB]
Get:118 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB]
Get:119 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.16-1 [116 kB]
Get:120 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:121 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB]
Get:122 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-5 [61.9 kB]
Get:123 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:124 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:125 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:126 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB]
Get:127 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 13.7 MB in 0s (153 MB/s)
Selecting previously unselected package netbase.
(Reading database ... 21274 files and directories currently installed.)
Preparing to unpack .../000-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../001-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package openssl.
Preparing to unpack .../002-openssl_3.0.8-1_amd64.deb ...
Unpacking openssl (3.0.8-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../003-ca-certificates_20230311_all.deb ...
Unpacking ca-certificates (20230311) ...
Selecting previously unselected package diffstat.
Preparing to unpack .../004-diffstat_1.65-1_amd64.deb ...
Unpacking diffstat (1.65-1) ...
Selecting previously unselected package libassuan0:amd64.
Preparing to unpack .../005-libassuan0_2.5.5-5_amd64.deb ...
Unpacking libassuan0:amd64 (2.5.5-5) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../006-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package gpgconf.
Preparing to unpack .../007-gpgconf_2.2.40-1.1_amd64.deb ...
Unpacking gpgconf (2.2.40-1.1) ...
Selecting previously unselected package libsqlite3-0:amd64.
Preparing to unpack .../008-libsqlite3-0_3.40.1-2_amd64.deb ...
Unpacking libsqlite3-0:amd64 (3.40.1-2) ...
Selecting previously unselected package gpg.
Preparing to unpack .../009-gpg_2.2.40-1.1_amd64.deb ...
Unpacking gpg (2.2.40-1.1) ...
Selecting previously unselected package iso-codes.
Preparing to unpack .../010-iso-codes_4.13.0-1_all.deb ...
Unpacking iso-codes (4.13.0-1) ...
Selecting previously unselected package libaliased-perl.
Preparing to unpack .../011-libaliased-perl_0.34-3_all.deb ...
Unpacking libaliased-perl (0.34-3) ...
Selecting previously unselected package libapt-pkg-perl.
Preparing to unpack .../012-libapt-pkg-perl_0.1.40+b2_amd64.deb ...
Unpacking libapt-pkg-perl (0.1.40+b2) ...
Selecting previously unselected package libb-hooks-op-check-perl:amd64.
Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ...
Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ...
Selecting previously unselected package libdynaloader-functions-perl.
Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ...
Unpacking libdynaloader-functions-perl (0.003-3) ...
Selecting previously unselected package libdevel-callchecker-perl:amd64.
Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2_amd64.deb ...
Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ...
Selecting previously unselected package libparams-classify-perl:amd64.
Preparing to unpack .../016-libparams-classify-perl_0.015-2+b1_amd64.deb ...
Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ...
Selecting previously unselected package libmodule-runtime-perl.
Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ...
Unpacking libmodule-runtime-perl (0.016-2) ...
Selecting previously unselected package libtry-tiny-perl.
Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ...
Unpacking libtry-tiny-perl (0.31-2) ...
Selecting previously unselected package libmodule-implementation-perl.
Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ...
Unpacking libmodule-implementation-perl (0.09-2) ...
Selecting previously unselected package libsub-exporter-progressive-perl.
Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ...
Unpacking libsub-exporter-progressive-perl (0.001013-3) ...
Selecting previously unselected package libvariable-magic-perl.
Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b1_amd64.deb ...
Unpacking libvariable-magic-perl (0.63-1+b1) ...
Selecting previously unselected package libb-hooks-endofscope-perl.
Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ...
Unpacking libb-hooks-endofscope-perl (0.26-1) ...
Selecting previously unselected package libberkeleydb-perl:amd64.
Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b1_amd64.deb ...
Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ...
Selecting previously unselected package libcapture-tiny-perl.
Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ...
Unpacking libcapture-tiny-perl (0.48-2) ...
Selecting previously unselected package libhtml-tagset-perl.
Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ...
Unpacking libhtml-tagset-perl (3.20-6) ...
Selecting previously unselected package libregexp-ipv6-perl.
Preparing to unpack .../026-libregexp-ipv6-perl_0.03-3_all.deb ...
Unpacking libregexp-ipv6-perl (0.03-3) ...
Selecting previously unselected package liburi-perl.
Preparing to unpack .../027-liburi-perl_5.17-1_all.deb ...
Unpacking liburi-perl (5.17-1) ...
Selecting previously unselected package libhtml-parser-perl:amd64.
Preparing to unpack .../028-libhtml-parser-perl_3.81-1_amd64.deb ...
Unpacking libhtml-parser-perl:amd64 (3.81-1) ...
Selecting previously unselected package libcgi-pm-perl.
Preparing to unpack .../029-libcgi-pm-perl_4.55-1_all.deb ...
Unpacking libcgi-pm-perl (4.55-1) ...
Selecting previously unselected package libclass-data-inheritable-perl.
Preparing to unpack .../030-libclass-data-inheritable-perl_0.08-3_all.deb ...
Unpacking libclass-data-inheritable-perl (0.08-3) ...
Selecting previously unselected package libclass-method-modifiers-perl.
Preparing to unpack .../031-libclass-method-modifiers-perl_2.14-1_all.deb ...
Unpacking libclass-method-modifiers-perl (2.14-1) ...
Selecting previously unselected package libclass-xsaccessor-perl.
Preparing to unpack .../032-libclass-xsaccessor-perl_1.19-4+b1_amd64.deb ...
Unpacking libclass-xsaccessor-perl (1.19-4+b1) ...
Selecting previously unselected package libclone-perl:amd64.
Preparing to unpack .../033-libclone-perl_0.46-1_amd64.deb ...
Unpacking libclone-perl:amd64 (0.46-1) ...
Selecting previously unselected package libconfig-tiny-perl.
Preparing to unpack .../034-libconfig-tiny-perl_2.28-2_all.deb ...
Unpacking libconfig-tiny-perl (2.28-2) ...
Selecting previously unselected package libparams-util-perl.
Preparing to unpack .../035-libparams-util-perl_1.102-2+b1_amd64.deb ...
Unpacking libparams-util-perl (1.102-2+b1) ...
Selecting previously unselected package libsub-install-perl.
Preparing to unpack .../036-libsub-install-perl_0.929-1_all.deb ...
Unpacking libsub-install-perl (0.929-1) ...
Selecting previously unselected package libdata-optlist-perl.
Preparing to unpack .../037-libdata-optlist-perl_0.113-1_all.deb ...
Unpacking libdata-optlist-perl (0.113-1) ...
Selecting previously unselected package libsub-exporter-perl.
Preparing to unpack .../038-libsub-exporter-perl_0.989-1_all.deb ...
Unpacking libsub-exporter-perl (0.989-1) ...
Selecting previously unselected package libconst-fast-perl.
Preparing to unpack .../039-libconst-fast-perl_0.014-2_all.deb ...
Unpacking libconst-fast-perl (0.014-2) ...
Selecting previously unselected package libcpanel-json-xs-perl:amd64.
Preparing to unpack .../040-libcpanel-json-xs-perl_4.35-1_amd64.deb ...
Unpacking libcpanel-json-xs-perl:amd64 (4.35-1) ...
Selecting previously unselected package libdevel-stacktrace-perl.
Preparing to unpack .../041-libdevel-stacktrace-perl_2.0400-2_all.deb ...
Unpacking libdevel-stacktrace-perl (2.0400-2) ...
Selecting previously unselected package libexception-class-perl.
Preparing to unpack .../042-libexception-class-perl_1.45-1_all.deb ...
Unpacking libexception-class-perl (1.45-1) ...
Selecting previously unselected package libiterator-perl.
Preparing to unpack .../043-libiterator-perl_0.03+ds1-2_all.deb ...
Unpacking libiterator-perl (0.03+ds1-2) ...
Selecting previously unselected package libiterator-util-perl.
Preparing to unpack .../044-libiterator-util-perl_0.02+ds1-2_all.deb ...
Unpacking libiterator-util-perl (0.02+ds1-2) ...
Selecting previously unselected package libdata-dpath-perl.
Preparing to unpack .../045-libdata-dpath-perl_0.58-2_all.deb ...
Unpacking libdata-dpath-perl (0.58-2) ...
Selecting previously unselected package libdata-messagepack-perl.
Preparing to unpack .../046-libdata-messagepack-perl_1.02-1+b1_amd64.deb ...
Unpacking libdata-messagepack-perl (1.02-1+b1) ...
Selecting previously unselected package libnet-domain-tld-perl.
Preparing to unpack .../047-libnet-domain-tld-perl_1.75-3_all.deb ...
Unpacking libnet-domain-tld-perl (1.75-3) ...
Selecting previously unselected package libdata-validate-domain-perl.
Preparing to unpack .../048-libdata-validate-domain-perl_0.10-1.1_all.deb ...
Unpacking libdata-validate-domain-perl (0.10-1.1) ...
Selecting previously unselected package libnet-ipv6addr-perl.
Preparing to unpack .../049-libnet-ipv6addr-perl_1.02-1_all.deb ...
Unpacking libnet-ipv6addr-perl (1.02-1) ...
Selecting previously unselected package libnet-netmask-perl.
Preparing to unpack .../050-libnet-netmask-perl_2.0002-2_all.deb ...
Unpacking libnet-netmask-perl (2.0002-2) ...
Selecting previously unselected package libnetaddr-ip-perl.
Preparing to unpack .../051-libnetaddr-ip-perl_4.079+dfsg-2+b1_amd64.deb ...
Unpacking libnetaddr-ip-perl (4.079+dfsg-2+b1) ...
Selecting previously unselected package libdata-validate-ip-perl.
Preparing to unpack .../052-libdata-validate-ip-perl_0.31-1_all.deb ...
Unpacking libdata-validate-ip-perl (0.31-1) ...
Selecting previously unselected package libdata-validate-uri-perl.
Preparing to unpack .../053-libdata-validate-uri-perl_0.07-2_all.deb ...
Unpacking libdata-validate-uri-perl (0.07-2) ...
Selecting previously unselected package libdevel-size-perl.
Preparing to unpack .../054-libdevel-size-perl_0.83-2+b1_amd64.deb ...
Unpacking libdevel-size-perl (0.83-2+b1) ...
Selecting previously unselected package libemail-address-xs-perl.
Preparing to unpack .../055-libemail-address-xs-perl_1.05-1+b1_amd64.deb ...
Unpacking libemail-address-xs-perl (1.05-1+b1) ...
Selecting previously unselected package libencode-locale-perl.
Preparing to unpack .../056-libencode-locale-perl_1.05-3_all.deb ...
Unpacking libencode-locale-perl (1.05-3) ...
Selecting previously unselected package libipc-system-simple-perl.
Preparing to unpack .../057-libipc-system-simple-perl_1.30-2_all.deb ...
Unpacking libipc-system-simple-perl (1.30-2) ...
Selecting previously unselected package libfile-basedir-perl.
Preparing to unpack .../058-libfile-basedir-perl_0.09-2_all.deb ...
Unpacking libfile-basedir-perl (0.09-2) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../059-libtimedate-perl_2.3300-2_all.deb ...
Unpacking libtimedate-perl (2.3300-2) ...
Selecting previously unselected package libhttp-date-perl.
Preparing to unpack .../060-libhttp-date-perl_6.05-2_all.deb ...
Unpacking libhttp-date-perl (6.05-2) ...
Selecting previously unselected package libfile-listing-perl.
Preparing to unpack .../061-libfile-listing-perl_6.15-1_all.deb ...
Unpacking libfile-listing-perl (6.15-1) ...
Selecting previously unselected package libfont-ttf-perl.
Preparing to unpack .../062-libfont-ttf-perl_1.06-2_all.deb ...
Unpacking libfont-ttf-perl (1.06-2) ...
Selecting previously unselected package libio-html-perl.
Preparing to unpack .../063-libio-html-perl_1.004-3_all.deb ...
Unpacking libio-html-perl (1.004-3) ...
Selecting previously unselected package liblwp-mediatypes-perl.
Preparing to unpack .../064-liblwp-mediatypes-perl_6.04-2_all.deb ...
Unpacking liblwp-mediatypes-perl (6.04-2) ...
Selecting previously unselected package libhttp-message-perl.
Preparing to unpack .../065-libhttp-message-perl_6.44-1_all.deb ...
Unpacking libhttp-message-perl (6.44-1) ...
Selecting previously unselected package libhtml-form-perl.
Preparing to unpack .../066-libhtml-form-perl_6.11-1_all.deb ...
Unpacking libhtml-form-perl (6.11-1) ...
Selecting previously unselected package libhtml-html5-entities-perl.
Preparing to unpack .../067-libhtml-html5-entities-perl_0.004-3_all.deb ...
Unpacking libhtml-html5-entities-perl (0.004-3) ...
Selecting previously unselected package libhtml-tree-perl.
Preparing to unpack .../068-libhtml-tree-perl_5.07-3_all.deb ...
Unpacking libhtml-tree-perl (5.07-3) ...
Selecting previously unselected package libhttp-cookies-perl.
Preparing to unpack .../069-libhttp-cookies-perl_6.10-1_all.deb ...
Unpacking libhttp-cookies-perl (6.10-1) ...
Selecting previously unselected package libhttp-negotiate-perl.
Preparing to unpack .../070-libhttp-negotiate-perl_6.01-2_all.deb ...
Unpacking libhttp-negotiate-perl (6.01-2) ...
Selecting previously unselected package perl-openssl-defaults:amd64.
Preparing to unpack .../071-perl-openssl-defaults_7+b1_amd64.deb ...
Unpacking perl-openssl-defaults:amd64 (7+b1) ...
Selecting previously unselected package libnet-ssleay-perl:amd64.
Preparing to unpack .../072-libnet-ssleay-perl_1.92-2+b1_amd64.deb ...
Unpacking libnet-ssleay-perl:amd64 (1.92-2+b1) ...
Selecting previously unselected package libio-socket-ssl-perl.
Preparing to unpack .../073-libio-socket-ssl-perl_2.081-2_all.deb ...
Unpacking libio-socket-ssl-perl (2.081-2) ...
Selecting previously unselected package libnet-http-perl.
Preparing to unpack .../074-libnet-http-perl_6.22-1_all.deb ...
Unpacking libnet-http-perl (6.22-1) ...
Selecting previously unselected package liblwp-protocol-https-perl.
Preparing to unpack .../075-liblwp-protocol-https-perl_6.10-1_all.deb ...
Unpacking liblwp-protocol-https-perl (6.10-1) ...
Selecting previously unselected package libwww-robotrules-perl.
Preparing to unpack .../076-libwww-robotrules-perl_6.02-1_all.deb ...
Unpacking libwww-robotrules-perl (6.02-1) ...
Selecting previously unselected package libwww-perl.
Preparing to unpack .../077-libwww-perl_6.68-1_all.deb ...
Unpacking libwww-perl (6.68-1) ...
Selecting previously unselected package libhtml-tokeparser-simple-perl.
Preparing to unpack .../078-libhtml-tokeparser-simple-perl_3.16-4_all.deb ...
Unpacking libhtml-tokeparser-simple-perl (3.16-4) ...
Selecting previously unselected package libimport-into-perl.
Preparing to unpack .../079-libimport-into-perl_1.002005-2_all.deb ...
Unpacking libimport-into-perl (1.002005-2) ...
Selecting previously unselected package libio-interactive-perl.
Preparing to unpack .../080-libio-interactive-perl_1.023-2_all.deb ...
Unpacking libio-interactive-perl (1.023-2) ...
Selecting previously unselected package libipc-run3-perl.
Preparing to unpack .../081-libipc-run3-perl_0.048-3_all.deb ...
Unpacking libipc-run3-perl (0.048-3) ...
Selecting previously unselected package libjson-maybexs-perl.
Preparing to unpack .../082-libjson-maybexs-perl_1.004004-1_all.deb ...
Unpacking libjson-maybexs-perl (1.004004-1) ...
Selecting previously unselected package liblist-compare-perl.
Preparing to unpack .../083-liblist-compare-perl_0.55-2_all.deb ...
Unpacking liblist-compare-perl (0.55-2) ...
Selecting previously unselected package liblist-someutils-perl.
Preparing to unpack .../084-liblist-someutils-perl_0.59-1_all.deb ...
Unpacking liblist-someutils-perl (0.59-1) ...
Selecting previously unselected package liblist-utilsby-perl.
Preparing to unpack .../085-liblist-utilsby-perl_0.12-2_all.deb ...
Unpacking liblist-utilsby-perl (0.12-2) ...
Selecting previously unselected package liblz1:amd64.
Preparing to unpack .../086-liblz1_1.13-5_amd64.deb ...
Unpacking liblz1:amd64 (1.13-5) ...
Selecting previously unselected package liblzo2-2:amd64.
Preparing to unpack .../087-liblzo2-2_2.10-2_amd64.deb ...
Unpacking liblzo2-2:amd64 (2.10-2) ...
Selecting previously unselected package libmarkdown2:amd64.
Preparing to unpack .../088-libmarkdown2_2.2.7-2_amd64.deb ...
Unpacking libmarkdown2:amd64 (2.2.7-2) ...
Selecting previously unselected package libmldbm-perl.
Preparing to unpack .../089-libmldbm-perl_2.05-4_all.deb ...
Unpacking libmldbm-perl (2.05-4) ...
Selecting previously unselected package librole-tiny-perl.
Preparing to unpack .../090-librole-tiny-perl_2.002004-1_all.deb ...
Unpacking librole-tiny-perl (2.002004-1) ...
Selecting previously unselected package libsub-quote-perl.
Preparing to unpack .../091-libsub-quote-perl_2.006008-1_all.deb ...
Unpacking libsub-quote-perl (2.006008-1) ...
Selecting previously unselected package libmoo-perl.
Preparing to unpack .../092-libmoo-perl_2.005005-1_all.deb ...
Unpacking libmoo-perl (2.005005-1) ...
Selecting previously unselected package libstrictures-perl.
Preparing to unpack .../093-libstrictures-perl_2.000006-1_all.deb ...
Unpacking libstrictures-perl (2.000006-1) ...
Selecting previously unselected package libmoox-aliases-perl.
Preparing to unpack .../094-libmoox-aliases-perl_0.001006-2_all.deb ...
Unpacking libmoox-aliases-perl (0.001006-2) ...
Selecting previously unselected package libmouse-perl.
Preparing to unpack .../095-libmouse-perl_2.5.10-1+b3_amd64.deb ...
Unpacking libmouse-perl (2.5.10-1+b3) ...
Selecting previously unselected package libpackage-stash-perl.
Preparing to unpack .../096-libpackage-stash-perl_0.40-1_all.deb ...
Unpacking libpackage-stash-perl (0.40-1) ...
Selecting previously unselected package libsub-identify-perl.
Preparing to unpack .../097-libsub-identify-perl_0.14-3_amd64.deb ...
Unpacking libsub-identify-perl (0.14-3) ...
Selecting previously unselected package libsub-name-perl:amd64.
Preparing to unpack .../098-libsub-name-perl_0.26-2+b1_amd64.deb ...
Unpacking libsub-name-perl:amd64 (0.26-2+b1) ...
Selecting previously unselected package libnamespace-clean-perl.
Preparing to unpack .../099-libnamespace-clean-perl_0.27-2_all.deb ...
Unpacking libnamespace-clean-perl (0.27-2) ...
Selecting previously unselected package libpath-tiny-perl.
Preparing to unpack .../100-libpath-tiny-perl_0.144-1_all.deb ...
Unpacking libpath-tiny-perl (0.144-1) ...
Selecting previously unselected package libperlio-gzip-perl.
Preparing to unpack .../101-libperlio-gzip-perl_0.20-1+b1_amd64.deb ...
Unpacking libperlio-gzip-perl (0.20-1+b1) ...
Selecting previously unselected package libperlio-utf8-strict-perl.
Preparing to unpack .../102-libperlio-utf8-strict-perl_0.010-1_amd64.deb ...
Unpacking libperlio-utf8-strict-perl (0.010-1) ...
Selecting previously unselected package libproc-processtable-perl:amd64.
Preparing to unpack .../103-libproc-processtable-perl_0.634-1+b2_amd64.deb ...
Unpacking libproc-processtable-perl:amd64 (0.634-1+b2) ...
Selecting previously unselected package libregexp-wildcards-perl.
Preparing to unpack .../104-libregexp-wildcards-perl_1.05-3_all.deb ...
Unpacking libregexp-wildcards-perl (1.05-3) ...
Selecting previously unselected package libsereal-decoder-perl.
Preparing to unpack .../105-libsereal-decoder-perl_5.003+ds-1_amd64.deb ...
Unpacking libsereal-decoder-perl (5.003+ds-1) ...
Selecting previously unselected package libsereal-encoder-perl.
Preparing to unpack .../106-libsereal-encoder-perl_5.003+ds-1_amd64.deb ...
Unpacking libsereal-encoder-perl (5.003+ds-1) ...
Selecting previously unselected package libsort-versions-perl.
Preparing to unpack .../107-libsort-versions-perl_1.62-3_all.deb ...
Unpacking libsort-versions-perl (1.62-3) ...
Selecting previously unselected package libxs-parse-keyword-perl.
Preparing to unpack .../108-libxs-parse-keyword-perl_0.33-1_amd64.deb ...
Unpacking libxs-parse-keyword-perl (0.33-1) ...
Selecting previously unselected package libsyntax-keyword-try-perl.
Preparing to unpack .../109-libsyntax-keyword-try-perl_0.28-1_amd64.deb ...
Unpacking libsyntax-keyword-try-perl (0.28-1) ...
Selecting previously unselected package libterm-readkey-perl.
Preparing to unpack .../110-libterm-readkey-perl_2.38-2+b1_amd64.deb ...
Unpacking libterm-readkey-perl (2.38-2+b1) ...
Selecting previously unselected package libtext-levenshteinxs-perl.
Preparing to unpack .../111-libtext-levenshteinxs-perl_0.03-5+b1_amd64.deb ...
Unpacking libtext-levenshteinxs-perl (0.03-5+b1) ...
Selecting previously unselected package libtext-markdown-discount-perl.
Preparing to unpack .../112-libtext-markdown-discount-perl_0.16-1_amd64.deb ...
Unpacking libtext-markdown-discount-perl (0.16-1) ...
Selecting previously unselected package libtext-xslate-perl:amd64.
Preparing to unpack .../113-libtext-xslate-perl_3.5.9-1+b2_amd64.deb ...
Unpacking libtext-xslate-perl:amd64 (3.5.9-1+b2) ...
Selecting previously unselected package libtime-duration-perl.
Preparing to unpack .../114-libtime-duration-perl_1.21-2_all.deb ...
Unpacking libtime-duration-perl (1.21-2) ...
Selecting previously unselected package libtime-moment-perl.
Preparing to unpack .../115-libtime-moment-perl_0.44-2+b1_amd64.deb ...
Unpacking libtime-moment-perl (0.44-2+b1) ...
Selecting previously unselected package libunicode-utf8-perl.
Preparing to unpack .../116-libunicode-utf8-perl_0.62-2_amd64.deb ...
Unpacking libunicode-utf8-perl (0.62-2) ...
Selecting previously unselected package libwww-mechanize-perl.
Preparing to unpack .../117-libwww-mechanize-perl_2.16-1_all.deb ...
Unpacking libwww-mechanize-perl (2.16-1) ...
Selecting previously unselected package libyaml-0-2:amd64.
Preparing to unpack .../118-libyaml-0-2_0.2.5-1_amd64.deb ...
Unpacking libyaml-0-2:amd64 (0.2.5-1) ...
Selecting previously unselected package libyaml-libyaml-perl.
Preparing to unpack .../119-libyaml-libyaml-perl_0.86+ds-1_amd64.deb ...
Unpacking libyaml-libyaml-perl (0.86+ds-1) ...
Selecting previously unselected package plzip.
Preparing to unpack .../120-plzip_1.10-5_amd64.deb ...
Unpacking plzip (1.10-5) ...
Selecting previously unselected package lzop.
Preparing to unpack .../121-lzop_1.04-2_amd64.deb ...
Unpacking lzop (1.04-2) ...
Selecting previously unselected package patchutils.
Preparing to unpack .../122-patchutils_0.4.2-1_amd64.deb ...
Unpacking patchutils (0.4.2-1) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../123-t1utils_1.41-4_amd64.deb ...
Unpacking t1utils (1.41-4) ...
Selecting previously unselected package unzip.
Preparing to unpack .../124-unzip_6.0-28_amd64.deb ...
Unpacking unzip (6.0-28) ...
Selecting previously unselected package lintian.
Preparing to unpack .../125-lintian_2.116.3_all.deb ...
Unpacking lintian (2.116.3) ...
Selecting previously unselected package sbuild-build-depends-lintian-dummy:mips64el.
Preparing to unpack .../126-sbuild-build-depends-lintian-dummy_0.invalid.0_mips64el.deb ...
Unpacking sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ...
Setting up libapt-pkg-perl (0.1.40+b2) ...
Setting up liblz1:amd64 (1.13-5) ...
Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ...
Setting up plzip (1.10-5) ...
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode
Setting up libunicode-utf8-perl (0.62-2) ...
Setting up libmouse-perl (2.5.10-1+b3) ...
Setting up libdata-messagepack-perl (1.02-1+b1) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libclass-method-modifiers-perl (2.14-1) ...
Setting up liblist-compare-perl (0.55-2) ...
Setting up libclone-perl:amd64 (0.46-1) ...
Setting up libyaml-0-2:amd64 (0.2.5-1) ...
Setting up libsub-identify-perl (0.14-3) ...
Setting up libcpanel-json-xs-perl:amd64 (4.35-1) ...
Setting up libhtml-tagset-perl (3.20-6) ...
Setting up libdevel-size-perl (0.83-2+b1) ...
Setting up unzip (6.0-28) ...
Setting up libsqlite3-0:amd64 (3.40.1-2) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libyaml-libyaml-perl (0.86+ds-1) ...
Setting up libio-interactive-perl (1.023-2) ...
Setting up libtry-tiny-perl (0.31-2) ...
Setting up perl-openssl-defaults:amd64 (7+b1) ...
Setting up libmldbm-perl (2.05-4) ...
Setting up liblzo2-2:amd64 (2.10-2) ...
Setting up libtime-moment-perl (0.44-2+b1) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libassuan0:amd64 (2.5.5-5) ...
Setting up libconfig-tiny-perl (2.28-2) ...
Setting up libsereal-encoder-perl (5.003+ds-1) ...
Setting up liblist-utilsby-perl (0.12-2) ...
Setting up libnet-netmask-perl (2.0002-2) ...
Setting up libsub-install-perl (0.929-1) ...
Setting up patchutils (0.4.2-1) ...
Setting up libjson-maybexs-perl (1.004004-1) ...
Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ...
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libxs-parse-keyword-perl (0.33-1) ...
Setting up libipc-system-simple-perl (1.30-2) ...
Setting up libnet-domain-tld-perl (1.75-3) ...
Setting up libperlio-utf8-strict-perl (0.010-1) ...
Setting up t1utils (1.41-4) ...
Setting up diffstat (1.65-1) ...
Setting up libvariable-magic-perl (0.63-1+b1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ...
Setting up libparams-util-perl (1.102-2+b1) ...
Setting up libtime-duration-perl (1.21-2) ...
Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ...
Setting up libsub-exporter-progressive-perl (0.001013-3) ...
Setting up libcapture-tiny-perl (0.48-2) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libregexp-ipv6-perl (0.03-3) ...
Setting up libsub-name-perl:amd64 (0.26-2+b1) ...
Setting up libsyntax-keyword-try-perl (0.28-1) ...
Setting up libdata-validate-domain-perl (0.10-1.1) ...
Setting up libproc-processtable-perl:amd64 (0.634-1+b2) ...
Setting up libpath-tiny-perl (0.144-1) ...
Setting up lzop (1.04-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libipc-run3-perl (0.048-3) ...
Setting up libregexp-wildcards-perl (1.05-3) ...
Setting up libaliased-perl (0.34-3) ...
Setting up netbase (6.4) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libdevel-stacktrace-perl (2.0400-2) ...
Setting up libclass-xsaccessor-perl (1.19-4+b1) ...
Setting up libsort-versions-perl (1.62-3) ...
Setting up libterm-readkey-perl (2.38-2+b1) ...
Setting up libfont-ttf-perl (1.06-2) ...
Setting up openssl (3.0.8-1) ...
Setting up libtext-levenshteinxs-perl (0.03-5+b1) ...
Setting up libperlio-gzip-perl (0.20-1+b1) ...
Setting up readline-common (8.2-1.3) ...
Setting up libhtml-html5-entities-perl (0.004-3) ...
Setting up libsereal-decoder-perl (5.003+ds-1) ...
Setting up libmarkdown2:amd64 (2.2.7-2) ...
Setting up liburi-perl (5.17-1) ...
Setting up iso-codes (4.13.0-1) ...
Setting up libnet-ipv6addr-perl (1.02-1) ...
Setting up libdata-validate-ip-perl (0.31-1) ...
Setting up libemail-address-xs-perl (1.05-1+b1) ...
Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ...
Setting up libhttp-date-perl (6.05-2) ...
Setting up libfile-basedir-perl (0.09-2) ...
Setting up libfile-listing-perl (6.15-1) ...
Setting up libreadline8:amd64 (8.2-1.3) ...
Setting up libnet-http-perl (6.22-1) ...
Setting up libtext-markdown-discount-perl (0.16-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.008-2) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up libdata-validate-uri-perl (0.07-2) ...
Setting up libdata-optlist-perl (0.113-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libhtml-parser-perl:amd64 (3.81-1) ...
Setting up gpgconf (2.2.40-1.1) ...
Setting up libio-socket-ssl-perl (2.081-2) ...
Setting up gpg (2.2.40-1.1) ...
Setting up libsub-exporter-perl (0.989-1) ...
Setting up libhttp-message-perl (6.44-1) ...
Setting up libhtml-form-perl (6.11-1) ...
Setting up libiterator-perl (0.03+ds1-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libiterator-util-perl (0.02+ds1-2) ...
Setting up libhttp-cookies-perl (6.10-1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b1) ...
Setting up libcgi-pm-perl (4.55-1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libconst-fast-perl (0.014-2) ...
Setting up libdata-dpath-perl (0.58-2) ...
Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblist-someutils-perl (0.59-1) ...
Setting up libmoox-aliases-perl (0.001006-2) ...
Setting up libb-hooks-endofscope-perl (0.26-1) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up libwww-perl (6.68-1) ...
Setting up libhtml-tokeparser-simple-perl (3.16-4) ...
Setting up libwww-mechanize-perl (2.16-1) ...
Setting up liblwp-protocol-https-perl (6.10-1) ...
Setting up lintian (2.116.3) ...
Setting up sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ...
Processing triggers for libc-bin (2.36-9) ...
Processing triggers for man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Running lintian...

I: Lintian run was successful.

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


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 408088
Build-Time: 454
Distribution: unstable
Foreign Architectures: mips64el
Host Architecture: mips64el
Install-Time: 9
Job: plink_1.07+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: plink
Package-Time: 471
Source-Version: 1.07+dfsg-4
Space: 408088
Status: successful
Version: 1.07+dfsg-4
--------------------------------------------------------------------------------
Finished at 2023-04-17T01:32:59Z
Build needed 00:07:51, 408088k disk space