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

+==============================================================================+
| plink 1.07+dfsg-4 (arm64)                    Sat, 02 Apr 2022 04:08:06 +0000 |
+==============================================================================+

Package: plink
Version: 1.07+dfsg-4
Source Version: 1.07+dfsg-4
Distribution: unstable
Machine Architecture: amd64
Host Architecture: arm64
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-0a6d8a0d-6eec-438d-abe0-068c15ae3142' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/plink-qdeszL/resolver-00gzEM' with '<<RESOLVERDIR>>'

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

Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2022-04-02-0203.55-F-2022-04-01-0806.30.pdiff [69.7 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2022-04-02-0203.55-F-2022-04-01-0806.30.pdiff [82.6 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2022-04-02-0203.55-F-2022-04-01-0806.30.pdiff [69.7 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2022-04-02-0203.55-F-2022-04-01-0806.30.pdiff [82.6 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8980 kB]
Fetched 9424 kB in 4s (2388 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  apt libapt-pkg6.0
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2525 kB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg6.0 amd64 2.4.4 [1029 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 apt amd64 2.4.4 [1496 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2525 kB in 0s (77.4 MB/s)
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(Reading database ... 10602 files and directories currently installed.)
Preparing to unpack .../libapt-pkg6.0_2.4.4_amd64.deb ...
Unpacking libapt-pkg6.0:amd64 (2.4.4) over (2.4.3) ...
Setting up libapt-pkg6.0:amd64 (2.4.4) ...
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(Reading database ... 10602 files and directories currently installed.)
Preparing to unpack .../archives/apt_2.4.4_amd64.deb ...
Unpacking apt (2.4.4) over (2.4.3) ...
Setting up apt (2.4.4) ...
Processing triggers for libc-bin (2.33-7) ...

+------------------------------------------------------------------------------+
| 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://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-4 (dsc) [2076 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-4 (tar) [429 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main plink 1.07+dfsg-4 (diff) [17.4 kB]
Fetched 449 kB in 0s (6005 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/plink-qdeszL/plink-1.07+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/plink-qdeszL' 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [411 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [500 B]
Fetched 1868 B in 0s (75.8 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu
  bsdextrautils build-essential cpp-11-aarch64-linux-gnu cpp-aarch64-linux-gnu
  cross-config crossbuild-essential-arm64 debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11
  g++-11-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-aarch64-linux-gnu
  gcc-11-aarch64-linux-gnu-base gcc-11-base:arm64 gcc-11-cross-base
  gcc-12-base:arm64 gcc-12-cross-base gcc-9-base:arm64 gcc-aarch64-linux-gnu
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libasan5:arm64 libasan6-arm64-cross libatomic1:arm64 libatomic1-arm64-cross
  libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64
  libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64
  libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-11-dev-arm64-cross libgcc-9-dev:arm64 libgcc-s1:arm64
  libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross
  libgssapi-krb5-2:arm64 libhwasan0-arm64-cross libicu67 libio-string-perl
  libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64
  libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64
  liblsan0-arm64-cross libmagic-mgc libmagic1 libnsl-dev libnsl-dev:arm64
  libnsl2:arm64 libperl5.34 libpipeline1 libsigsegv2 libssl1.1:arm64
  libstdc++-11-dev libstdc++-11-dev-arm64-cross libstdc++-9-dev:arm64
  libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev
  libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64
  libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64
  linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.34 po-debconf
  rpcsvc-proto sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales
  cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib
  g++-11-multilib gcc-11-doc manpages-dev flex bison gdb-aarch64-linux-gnu
  gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64
  libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64
  glibc-doc manpages-dev:arm64 gnupg git bzr krb5-doc:arm64 krb5-user:arm64
  libstdc++-11-doc libstdc++-9-doc:arm64 libtool-doc gfortran
  | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less
  www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl
  libtap-harness-archive-perl libmail-box-perl
Recommended packages:
  gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:arm64
  libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:arm64 libltdl-dev
  libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl
  netbase libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu
  bsdextrautils build-essential cpp-11-aarch64-linux-gnu cpp-aarch64-linux-gnu
  cross-config crossbuild-essential-arm64 debhelper dh-autoreconf
  dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11
  g++-11-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-aarch64-linux-gnu
  gcc-11-aarch64-linux-gnu-base gcc-11-base:arm64 gcc-11-cross-base
  gcc-12-base:arm64 gcc-12-cross-base gcc-9-base:arm64 gcc-aarch64-linux-gnu
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libasan5:arm64 libasan6-arm64-cross libatomic1:arm64 libatomic1-arm64-cross
  libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64
  libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64
  libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-11-dev-arm64-cross libgcc-9-dev:arm64 libgcc-s1:arm64
  libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross
  libgssapi-krb5-2:arm64 libhwasan0-arm64-cross libicu67 libio-string-perl
  libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64
  libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64
  liblsan0-arm64-cross libmagic-mgc libmagic1 libnsl-dev libnsl-dev:arm64
  libnsl2:arm64 libperl5.34 libpipeline1 libsigsegv2 libssl1.1:arm64
  libstdc++-11-dev libstdc++-11-dev-arm64-cross libstdc++-9-dev:arm64
  libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev
  libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64
  libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64
  linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.34 po-debconf
  rpcsvc-proto sbuild-build-depends-main-dummy:arm64 sensible-utils ucf
  zlib1g:arm64 zlib1g-dev:arm64
0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded.
Need to get 118 MB of archives.
After this operation, 488 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://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.34 all 5.34.0-3 [2850 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.34 amd64 5.34.0-3 [4208 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.34.0-3 [297 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b2 [19.2 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.4.0-5 [200 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.41-3 [295 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.41-3 [130 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.41-3 [67.0 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-6 [175 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-8 [936 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.3-1+b1 [144 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.5-1 [37.6 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.10.2-1 [1411 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-6 [510 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.38-3 [3265 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.27-1.1 [118 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.33-7 [2289 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev amd64 11.2.0-19 [1958 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11 amd64 11.2.0-19 [10.2 MB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:11.2.0-2 [1636 B]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.21.7 [1611 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.21.7 [2354 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-aarch64-linux-gnu-base amd64 11.2.0-18cross1 [208 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-11-aarch64-linux-gnu amd64 11.2.0-18cross1 [8493 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:11.2.0-2 [17.0 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base all 11.2.0-18cross1 [203 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-12-cross-base all 12-20220222-1cross1 [202 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.33-1cross1 [1243 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-arm64-cross all 12-20220222-1cross1 [35.1 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 12-20220222-1cross1 [102 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 12-20220222-1cross1 [23.4 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 12-20220222-1cross1 [9244 B]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-arm64-cross all 11.2.0-18cross1 [1941 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 12-20220222-1cross1 [925 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 11.2.0-18cross1 [1949 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 12-20220222-1cross1 [517 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 12-20220222-1cross1 [860 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libhwasan0-arm64-cross all 12-20220222-1cross1 [997 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-11-dev-arm64-cross all 11.2.0-18cross1 [933 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-aarch64-linux-gnu amd64 11.2.0-18cross1 [16.8 MB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:11.2.0-2 [1456 B]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.15.5-1cross1 [1554 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.33-1cross1 [1938 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev-arm64-cross all 11.2.0-18cross1 [1917 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11-aarch64-linux-gnu amd64 11.2.0-18cross1 [9380 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:11.2.0-2 [1176 B]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.13+dfsg-1 [709 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1 [337 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.9 [6708 B]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.6 [193 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.7-2 [526 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.186-1 [179 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-6 [1310 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.6 [1054 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-11-base arm64 11.2.0-19 [208 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-12-base arm64 12-20220319-1 [206 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-s1 arm64 12-20220319-1 [35.1 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.33-7 [2478 kB]
Get:94 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.4.0-5 [2673 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 12-20220319-1 [9516 B]
Get:96 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.16.18-1 [1495 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt1 arm64 1:4.4.27-1.1 [90.7 kB]
Get:98 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.27-1.1 [121 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main arm64 libcom-err2 arm64 1.46.5-2 [75.5 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5support0 arm64 1.19.2-2+b1 [65.2 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main arm64 libk5crypto3 arm64 1.19.2-2+b1 [114 kB]
Get:102 http://debian.oregonstate.edu/debian unstable/main arm64 libkeyutils1 arm64 1.6.1-3 [15.4 kB]
Get:103 http://debian.oregonstate.edu/debian unstable/main arm64 libssl1.1 arm64 1.1.1n-1 [1387 kB]
Get:104 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5-3 arm64 1.19.2-2+b1 [346 kB]
Get:105 http://debian.oregonstate.edu/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.19.2-2+b1 [157 kB]
Get:106 http://debian.oregonstate.edu/debian unstable/main arm64 libtirpc3 arm64 1.3.2-2 [80.4 kB]
Get:107 http://debian.oregonstate.edu/debian unstable/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB]
Get:108 http://debian.oregonstate.edu/debian unstable/main arm64 libtirpc-dev arm64 1.3.2-2 [193 kB]
Get:109 http://debian.oregonstate.edu/debian unstable/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB]
Get:110 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.33-7 [1941 kB]
Get:111 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 12-20220319-1 [104 kB]
Get:112 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 12-20220319-1 [23.8 kB]
Get:113 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 12-20220319-1 [926 kB]
Get:114 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 11.2.0-19 [1956 kB]
Get:115 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 12-20220319-1 [558 kB]
Get:116 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 12-20220319-1 [861 kB]
Get:117 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.4.0-5 [886 kB]
Get:118 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.4.0-5 [1678 kB]
Get:119 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g arm64 1:1.2.11.dfsg-4 [88.0 kB]
Get:120 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-4 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libconfig-inifiles-perl (3.000003-1) ...
Setting up libpipeline1:amd64 (1.5.5-1) ...
Setting up gcc-11-aarch64-linux-gnu-base:amd64 (11.2.0-18cross1) ...
Setting up gcc-11-base:arm64 (11.2.0-19) ...
Setting up gcc-12-cross-base (12-20220222-1cross1) ...
Setting up bsdextrautils (2.37.3-1+b1) ...
Setting up libicu67:amd64 (67.1-7) ...
Setting up libmagic-mgc (1:5.41-3) ...
Setting up libmagic1:amd64 (1:5.41-3) ...
Setting up linux-libc-dev:arm64 (5.16.18-1) ...
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Setting up binutils-aarch64-linux-gnu (2.38-3) ...
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Setting up perl-modules-5.34 (5.34.0-3) ...
Setting up gcc-12-base:arm64 (12-20220319-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up cross-config (2.6.18+nmu2) ...
Setting up libtirpc-dev:amd64 (1.3.2-2) ...
Setting up rpcsvc-proto (1.4.2-4) ...
Setting up libsigsegv2:amd64 (2.14-1) ...
Setting up libc6-arm64-cross (2.33-1cross1) ...
Setting up autopoint (0.21-6) ...
Setting up libitm1-arm64-cross (12-20220222-1cross1) ...
Setting up linux-libc-dev-arm64-cross (5.15.5-1cross1) ...
Setting up cpp-11-aarch64-linux-gnu (11.2.0-18cross1) ...
Setting up gcc-11-cross-base (11.2.0-18cross1) ...
Setting up libnsl-dev:amd64 (1.3.0-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libcrypt-dev:amd64 (1:4.4.27-1.1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libc6-dev:amd64 (2.33-7) ...
Setting up libelf1:amd64 (0.186-1) ...
Setting up libxml2:amd64 (2.9.13+dfsg-1) ...
Setting up liblocale-gettext-perl (1.07-4+b2) ...
Setting up gcc-9-base:arm64 (9.4.0-5) ...
Setting up libgcc-s1-arm64-cross (12-20220222-1cross1) ...
Setting up libatomic1-arm64-cross (12-20220222-1cross1) ...
Setting up liblsan0-arm64-cross (12-20220222-1cross1) ...
Setting up libgomp1-arm64-cross (12-20220222-1cross1) ...
Setting up libperl5.34:amd64 (5.34.0-3) ...
Setting up gettext (0.21-6) ...
Setting up libtool (2.4.7-2) ...
Setting up libasan6-arm64-cross (11.2.0-18cross1) ...
Setting up libtsan0-arm64-cross (11.2.0-18cross1) ...
Setting up m4 (1.4.18-5) ...
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Setting up libc6-dev-arm64-cross (2.33-1cross1) ...
Setting up libstdc++6-arm64-cross (12-20220222-1cross1) ...
Setting up perl (5.34.0-3) ...
Setting up cpp-aarch64-linux-gnu (4:11.2.0-2) ...
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Setting up libdpkg-perl (1.21.7) ...
Setting up autoconf (2.71-2) ...
Setting up libstdc++-11-dev:amd64 (11.2.0-19) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up libsub-override-perl (0.09-2) ...
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-which-perl (1.23-1) ...
Setting up libubsan1-arm64-cross (12-20220222-1cross1) ...
Setting up g++-11 (11.2.0-19) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.6) ...
Setting up libxml-namespacesupport-perl (1.12-1.1) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libyaml-perl (1.30-1) ...
Setting up dpkg-dev (1.21.7) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libgcc-11-dev-arm64-cross (11.2.0-18cross1) ...
Setting up dh-autoreconf (20) ...
Setting up libxml-sax-base-perl (1.09-1.1) ...
Setting up libio-string-perl (1.08-3.1) ...
Setting up g++ (4:11.2.0-2) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.9) ...
Setting up libfile-homedir-perl (1.006-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gcc-11-aarch64-linux-gnu (11.2.0-18cross1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libstdc++-11-dev-arm64-cross (11.2.0-18cross1) ...
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 g++-11-aarch64-linux-gnu (11.2.0-18cross1) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up gcc-aarch64-linux-gnu (4:11.2.0-2) ...
Setting up debhelper (13.6) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up g++-aarch64-linux-gnu (4:11.2.0-2) ...
Setting up libconfig-auto-perl (0.44-1.1) ...
Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ...
Setting up dpkg-cross (2.6.18+nmu2) ...
Setting up crossbuild-essential-arm64 (12.9) ...
Setting up libgcc-s1:arm64 (12-20220319-1) ...
Setting up libc6:arm64 (2.33-7) ...
Setting up libstdc++6:arm64 (12-20220319-1) ...
Setting up liblsan0:arm64 (12-20220319-1) ...
Setting up libitm1:arm64 (12-20220319-1) ...
Setting up libtsan0:arm64 (11.2.0-19) ...
Setting up libkeyutils1:arm64 (1.6.1-3) ...
Setting up libssl1.1:arm64 (1.1.1n-1) ...
Setting up zlib1g:arm64 (1:1.2.11.dfsg-4) ...
Setting up libcrypt1:arm64 (1:4.4.27-1.1) ...
Setting up libcom-err2:arm64 (1.46.5-2) ...
Setting up libgomp1:arm64 (12-20220319-1) ...
Setting up libkrb5support0:arm64 (1.19.2-2+b1) ...
Setting up libasan5:arm64 (9.4.0-5) ...
Setting up libatomic1:arm64 (12-20220319-1) ...
Setting up libk5crypto3:arm64 (1.19.2-2+b1) ...
Setting up libubsan1:arm64 (12-20220319-1) ...
Setting up libcrypt-dev:arm64 (1:4.4.27-1.1) ...
Setting up libkrb5-3:arm64 (1.19.2-2+b1) ...
Setting up libgcc-9-dev:arm64 (9.4.0-5) ...
Setting up libgssapi-krb5-2:arm64 (1.19.2-2+b1) ...
Setting up libtirpc3:arm64 (1.3.2-2) ...
Setting up libtirpc-dev:arm64 (1.3.2-2) ...
Setting up libnsl2:arm64 (1.3.0-2) ...
Setting up libnsl-dev:arm64 (1.3.0-2) ...
Setting up libc6-dev:arm64 (2.33-7) ...
Setting up libstdc++-9-dev:arm64 (9.4.0-5) ...
Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-4) ...
Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7) ...

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

Arch check ok (arm64 included in any)

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

Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64)
Toolchain package versions: binutils_2.38-3 dpkg-dev_1.21.7 g++-11_11.2.0-19 gcc-11_11.2.0-19 libc6-dev_2.33-7 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-arm64-cross_11.2.0-18cross1 libstdc++-9-dev_9.4.0-5 libstdc++6_12-20220319-1 libstdc++6-arm64-cross_12-20220222-1cross1 linux-libc-dev_5.16.18-1
Package versions: adduser_3.121 apt_2.4.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3 binutils-aarch64-linux-gnu_2.38-3 binutils-common_2.38-3 binutils-x86-64-linux-gnu_2.38-3 bsdextrautils_2.37.3-1+b1 bsdutils_1:2.37.3-1+b1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-19 cpp-11-aarch64-linux-gnu_11.2.0-18cross1 cpp-8_8.4.0-7 cpp-aarch64-linux-gnu_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-arm64_12.9 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.6 debian-archive-keyring_2021.1.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dpkg_1.21.7 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.7 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.28-1 fdisk_2.37.3-1+b1 file_1:5.41-3 findutils_4.9.0-2 g++_4:11.2.0-2 g++-11_11.2.0-19 g++-11-aarch64-linux-gnu_11.2.0-18cross1 g++-aarch64-linux-gnu_4:11.2.0-2 gcc_4:11.2.0-2 gcc-11_11.2.0-19 gcc-11-aarch64-linux-gnu_11.2.0-18cross1 gcc-11-aarch64-linux-gnu-base_11.2.0-18cross1 gcc-11-base_11.2.0-19 gcc-11-cross-base_11.2.0-18cross1 gcc-12-base_12-20220319-1 gcc-12-cross-base_12-20220222-1cross1 gcc-8-base_8.4.0-7 gcc-9-base_9.4.0-5 gcc-aarch64-linux-gnu_4:11.2.0-2 gettext_0.21-6 gettext-base_0.21-6 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.4.4 libarchive-zip-perl_1.68-1 libasan5_9.4.0-5 libasan6_11.2.0-19 libasan6-arm64-cross_11.2.0-18cross1 libatomic1_12-20220319-1 libatomic1-arm64-cross_12-20220222-1cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3 libblkid1_2.37.3-1+b1 libbz2-1.0_1.0.8-5 libc-bin_2.33-7 libc-dev-bin_2.33-7 libc6_2.33-7 libc6-arm64-cross_2.33-1cross1 libc6-dev_2.33-7 libc6-dev-arm64-cross_2.33-1cross1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1 libcom-err2_1.46.5-2 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3 libctf0_2.38-3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.21.7 libelf1_0.186-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libfdisk1_2.37.3-1+b1 libffi6_3.2.1-9 libffi8_3.4.2-4 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.13.0-1 libfile-which-perl_1.23-1 libgcc-11-dev_11.2.0-19 libgcc-11-dev-arm64-cross_11.2.0-18cross1 libgcc-9-dev_9.4.0-5 libgcc-s1_12-20220319-1 libgcc-s1-arm64-cross_12-20220222-1cross1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4+b1 libgomp1_12-20220319-1 libgomp1-arm64-cross_12-20220222-1cross1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b1 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.7.3-1 libhwasan0-arm64-cross_12-20220222-1cross1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl19_0.20-2 libisl23_0.24-2 libitm1_12-20220319-1 libitm1-arm64-cross_12-20220222-1cross1 libk5crypto3_1.19.2-2+b1 libkeyutils1_1.6.1-3 libkrb5-3_1.19.2-2+b1 libkrb5support0_1.19.2-2+b1 liblocale-gettext-perl_1.07-4+b2 liblsan0_12-20220319-1 liblsan0-arm64-cross_12-20220222-1cross1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-3 libmagic1_1:5.41-3 libmount1_2.37.3-1+b1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmpx2_8.4.0-7 libncursesw6_6.3-2 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.28_5.28.1-6 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libquadmath0_12-20220319-1 libreadline8_8.1.2-1 libseccomp2_2.5.3-2 libselinux1_3.3-1+b2 libsemanage-common_3.3-1 libsemanage1_3.1-2 libsemanage2_3.3-1+b2 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1+b1 libss2_1.46.5-2 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.2.0-19 libstdc++-11-dev-arm64-cross_11.2.0-18cross1 libstdc++-9-dev_9.4.0-5 libstdc++6_12-20220319-1 libstdc++6-arm64-cross_12-20220222-1cross1 libsub-override-perl_0.09-2 libsystemd0_250.4-1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-2 libtsan0_11.2.0-19 libtsan0-arm64-cross_11.2.0-18cross1 libubsan1_12-20220319-1 libubsan1-arm64-cross_12-20220222-1cross1 libuchardet0_0.0.7-1 libudev1_250.4-1 libunistring2_1.0-1 libuuid1_2.37.3-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.13+dfsg-1 libxxhash0_0.8.1-1 libyaml-perl_1.30-1 libzstd1_1.4.9+dfsg-1 linux-libc-dev_5.16.18-1 linux-libc-dev-arm64-cross_5.15.5-1cross1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3+b1 mount_2.37.3-1+b1 ncurses-base_6.3-2 ncurses-bin_6.3-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.28_5.28.1-6 perl-modules-5.34_5.34.0-3 po-debconf_1.0.21+nmu1 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2022a-1 ucf_3.0043 util-linux_2.37.3-1+b1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4

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


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

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

Format: 3.0 (quilt)
Source: plink
Binary: plink
Architecture: any
Version: 1.07+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Andreas Tille <tille@debian.org>, Charles Plessy <plessy@debian.org>, Dylan Aïssi <daissi@debian.org>
Homepage: http://zzz.bwh.harvard.edu/plink/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/plink
Vcs-Git: https://salsa.debian.org/med-team/plink.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), zlib1g-dev
Package-List:
 plink deb science optional arch=any
Checksums-Sha1:
 c91f5de3a92ce44319870668dd81f34e076e9a38 429164 plink_1.07+dfsg.orig.tar.xz
 30da84e59157c428d54473d7e242e394a2dc6aaf 17356 plink_1.07+dfsg-4.debian.tar.xz
Checksums-Sha256:
 e11a1573101ca1a930f44db02050cd27790fec055fc6abcc0ebaad59fc99a5dd 429164 plink_1.07+dfsg.orig.tar.xz
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Files:
 fe49f1c648e5f318a9d4cdb23e343892 429164 plink_1.07+dfsg.orig.tar.xz
 d4701d1cd62de5c466ad92f54f17c8c8 17356 plink_1.07+dfsg-4.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.3xedh97X/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 31 15:36:45 2021 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./plink_1.07+dfsg-4.dsc
dpkg-source: info: extracting plink in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking plink_1.07+dfsg.orig.tar.xz
dpkg-source: info: unpacking plink_1.07+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 30_endiandetection.patch
dpkg-source: info: applying gcc-4.7.patch
dpkg-source: info: applying Fix_spelling_error.patch
dpkg-source: info: applying gcc11.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1003
SCHROOT_GROUP=helmut
SCHROOT_SESSION_ID=unstable-amd64-sbuild-0a6d8a0d-6eec-438d-abe0-068c15ae3142
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage -aarm64 -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 aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc "CXXFLAGS=-Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3" FORCE_DYNAMIC=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c plink.cpp
In file included from plink.cpp:28:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                   ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c options.cpp
In file included from options.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c input.cpp
In file included from input.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 in this function [-Wmaybe-uninitialized]
   91 |           if ( feof(PED) )
      |                ~~~~^~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c binput.cpp
In file included from binput.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                    ~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tinput.cpp
In file included from tinput.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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() )
      |            ~~~^~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genome.cpp
In file included from genome.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |       ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c helper.cpp
In file included from helper.h:24,
                 from helper.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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:378:48: warning: control reaches end of non-void function [-Wreturn-type]
  378 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘long unsigned int getLongUnsignedInt(std::string, std::string)’:
helper.cpp:391:48: warning: control reaches end of non-void function [-Wreturn-type]
  391 |       error("Not valid integer argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘double getDouble(std::string, std::string)’:
helper.cpp:404:48: warning: control reaches end of non-void function [-Wreturn-type]
  404 |       error("Not valid numeric argument for : "+a+" [ "+s+" ]");
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
helper.cpp: In function ‘std::vector<bool> vif_prune(std::vector<std::vector<double> >, double, std::vector<int>&)’:
helper.cpp:1405:11: warning: ‘maxI’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1405 |       int maxI;
      |           ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c stats.cpp
In file included from helper.h:24,
                 from stats.cpp:30:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                   ~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c filters.cpp
In file included from filters.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |       ^
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c locus.cpp
In file included from locus.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multi.cpp
In file included from multi.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |        ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c crandom.cpp
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cluster.cpp
In file included from helper.h:24,
                 from cluster.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                        ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mds.cpp
In file included from mds.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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);
      |        ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c output.cpp
In file included from output.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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:144:61: warning: ‘i1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  144 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i1,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp:145:61: warning: ‘i2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  145 |           << setw(par::pp_maxfid+par::pp_maxiid) << genotype(*this,i2,l) << " "
      |                                                     ~~~~~~~~^~~~~~~~~~~~
output.cpp: In member function ‘void Plink::display_indivReport()’:
output.cpp:69:32: warning: ‘i1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   69 |          << setw(6) << genotype(*this,i1,l) << "\n";
      |                        ~~~~~~~~^~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c informative.cpp
In file included from informative.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                        ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c assoc.cpp
In file included from helper.h:24,
                 from assoc.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 in this function [-Wmaybe-uninitialized]
 1109 |             pS->profileTestSNPInformation( l, log(odds[l]) * -log10( pvalue ) );
      |                                                               ~~~~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c epi.cpp
In file included from epi.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |           ^
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c prephap.cpp
In file included from prephap.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c phase.cpp
In file included from phase.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                       ~~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c trio.cpp
In file included from trio.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tdt.cpp
In file included from tdt.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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:937:40: warning: ‘zt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  937 |                   double OR_upper = exp( log(OR) + zt * sqrt(1/t1+1/t2)) ;
      |                                     ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sharing.cpp
In file included from perm.h:17,
                 from sharing.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genepi.cpp
In file included from genepi.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |        ^~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sets.cpp
In file included from sets.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c perm.cpp
In file included from perm.h:17,
                 from perm.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                                        ~^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mh.cpp
In file included from perm.h:17,
                 from mh.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 | }
      | ^
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genedrop.cpp
In file included from perm.h:17,
                 from genedrop.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gxe.cpp
In file included from helper.h:24,
                 from gxe.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c merge.cpp
In file included from merge.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 in this function [-Wmaybe-uninitialized]
 1103 |   if (write)
      |   ^~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hotel.cpp
In file included from hotel.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c multiple.cpp
In file included from helper.h:24,
                 from multiple.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploCC.cpp
In file included from haploCC.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 ) )
      |                                        ~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploTDT.cpp
In file included from haploTDT.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c poo.cpp
In file included from poo.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |          ^~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c webcheck.cpp
In file included from helper.h:24,
                 from webcheck.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qfam.cpp
In file included from helper.h:24,
                 from qfam.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |          ^~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linear.cpp
In file included from helper.h:24,
                 from linear.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |        ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c bmerge.cpp
In file included from bmerge.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                         ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c parse.cpp
In file included from parse.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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)
      |      ^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c mishap.cpp
In file included from mishap.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c legacy.cpp
In file included from helper.h:24,
                 from legacy.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~^~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c homozyg.cpp
In file included from helper.h:24,
                 from homozyg.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c segment.cpp
In file included from helper.h:24,
                 from segment.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 )
      |                     ~~~~~~~~~~~~~^~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c model.cpp
In file included from model.cpp:15:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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");
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c logistic.cpp
In file included from helper.h:24,
                 from logistic.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |        ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c glm.cpp
In file included from helper.h:24,
                 from glm.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 in this function [-Wmaybe-uninitialized]
  610 |           double pvalue = chiprobP(chisq,df);
      |                           ~~~~~~~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dcdflib.cpp
dcdflib.cpp: In function ‘void cdfbin(int*, double*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:1882:36: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 1882 |     if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160;
      |                        ~~~~~~~~~~~~^~~~~~~~~~~
dcdflib.cpp: In function ‘void cdfgam(int*, double*, double*, double*, double*, double*, int*, double*)’:
dcdflib.cpp:3544:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 3544 |         if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280;
      |              ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0000(int, int*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*, double*, double*, double*)’:
dcdflib.cpp:6025:23: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6025 |     if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp:6088:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6088 |     qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0;
      |           ~~~~~~^~~~~~~~~~~~~
dcdflib.cpp:6112:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6112 |     qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0;
      |            ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6153:18: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6153 |     qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0;
      |            ~~~~~~^~~~~~~~~~~~~~
dcdflib.cpp:6020:56: warning: variable ‘qok’ set but not used [-Wunused-but-set-variable]
 6020 | static unsigned long qbdd,qcond,qdum1,qdum2,qincr,qlim,qok,qup;
      |                                                        ^~~
dcdflib.cpp: In function ‘double dlanor(double*)’:
dcdflib.cpp:6401:28: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6401 |     if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘double dstrem(double*)’:
dcdflib.cpp:6782:29: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 6782 |     if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dcdflib.cpp: In function ‘void E0001(int, int*, double*, double*, double*, double*, long unsigned int*, long unsigned int*, double*, double*, double*, double*)’:
dcdflib.cpp:6996:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 6996 |     qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0;
      |              ~~~~~~~~~~~~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c elf.cpp
In file included from helper.h:24,
                 from elf.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In function ‘void displayScoresRegion(std::ofstream&, RCount&)’:
elf.cpp:493:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  493 |       for ( int k = 0 ; k < i->second.size(); k++)
      |                         ~~^~~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘void Plink::permTestRareDistribution(Perm&)’:
elf.cpp:609:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |   for (int l=0; l< original.size(); l++)
      |                 ~^~~~~~~~~~~~~~~~~
elf.cpp: In member function ‘vector_t Plink::testRareDistribution(Perm&, bool, std::map<Range, int2>&)’:
elf.cpp:654:16: warning: unused variable ‘pthresh’ [-Wunused-variable]
  654 |   const double pthresh = 0.01;
      |                ^~~~~~~
elf.cpp:655:8: warning: unused variable ‘one_sided’ [-Wunused-variable]
  655 |   bool one_sided = true;
      |        ^~~~~~~~~
elf.cpp:707:7: warning: unused variable ‘srange_cnt’ [-Wunused-variable]
  707 |   int srange_cnt = 0;
      |       ^~~~~~~~~~
elf.cpp:708:8: warning: unused variable ‘inRange’ [-Wunused-variable]
  708 |   bool inRange = false;
      |        ^~~~~~~
elf.cpp: In member function ‘void Plink::displayRareRange()’:
elf.cpp:895:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  895 |   for (int i = 0 ; i < tokens.size() ; i++)
      |                    ~~^~~~~~~~~~~~~~~
elf.cpp:939:26: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  939 |       if ( tokens.size() != ncol )
      |            ~~~~~~~~~~~~~~^~~~~~~
elf.cpp: In member function ‘bool RCount::addSNP(int)’:
elf.cpp:374:10: warning: ‘wt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  374 |   double wt;
      |          ^~
elf.cpp: In member function ‘void Plink::elfBaseline()’:
elf.cpp:1154:15: warning: ‘p_gcnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1154 |               ++(*p_gcnt);
      |               ^~~~~~~~~~~
elf.cpp:1165:19: warning: ‘p_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1165 |                   ++(*p_cnt);
      |                   ^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dfam.cpp
In file included from dfam.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |           ^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c fisher.cpp
In file included from helper.h:24,
                 from fisher.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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.");
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c linput.cpp
In file included from linput.cpp:25:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c sockets.cpp
In file included from helper.h:24,
                 from sockets.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |       ^~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup.cpp
In file included from helper.h:24,
                 from lookup.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                          ~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c proxy.cpp
In file included from proxy.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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];
      |          ^
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c pdriver.cpp
In file included from pdriver.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |           ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haploQTL.cpp
In file included from haploQTL.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                            ~~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplohelper.cpp
In file included from haplohelper.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c haplowindow.cpp
In file included from haplowindow.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                                  ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genogroup.cpp
In file included from genogroup.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                   ~^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nonfounderphasing.cpp
In file included from nonfounderphasing.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |              ^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c clumpld.cpp
In file included from helper.h:24,
                 from clumpld.h:21,
                 from clumpld.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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)
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c genoerr.cpp
In file included from genoerr.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                          ~~^~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c em.cpp
In file included from em.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                                   ~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c impute.cpp
In file included from impute.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~~^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaem.cpp
In file included from metaem.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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)
      |                  ~^~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c profile.cpp
In file included from profile.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                 ~^~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c nlist.cpp
In file included from helper.h:24,
                 from nlist.h:21,
                 from nlist.cpp:17:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 )
      |                 ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c whap.cpp
In file included from helper.h:24,
                 from whap.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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() )
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c simul.cpp
In file included from helper.h:24,
                 from simul.cpp:16:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |                              ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c gvar.cpp
In file included from helper.h:24,
                 from gvar.cpp:15:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                       ~^~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnv.cpp
In file included from helper.h:24,
                 from cnv.cpp:23:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 ];
      |          ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c step.cpp
In file included from helper.h:24,
                 from step.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c greport.cpp
In file included from greport.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |       ^~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c flip.cpp
In file included from helper.h:24,
                 from flip.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c qualscores.cpp
In file included from helper.h:24,
                 from qualscores.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |            ^~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cnvqt.cpp
In file included from helper.h:24,
                 from cnvqt.cpp:22:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c cfamily.cpp
In file included from cfamily.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                        ~~^~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c setscreen.cpp
In file included from setscreen.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c idhelp.cpp
In file included from idhelp.cpp:18:
idhelp.h: In member function ‘void IDGroup::display()’:
idhelp.h:196:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IDValue*>::size_type’ {aka ‘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++ )
      |                            ~~^~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c tag.cpp
In file included from helper.h:24,
                 from tag.cpp:24:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c hapglm.cpp
In file included from helper.h:24,
                 from hapglm.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~^~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c lookup2.cpp
In file included from helper.h:24,
                 from lookup2.cpp:18:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                     ~~^~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c blox.cpp
In file included from blox.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from blox.cpp:23:
phase.h: In member function ‘void HaploPhase::reset()’:
phase.h:252:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<bool> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |       for (int i=0; i<hap.size(); i++)
      |                     ~^~~~~~~~~~~
blox.cpp: In member function ‘std::map<Range, std::vector<int> > Plink::mkBlks(int, int)’:
blox.cpp:147:11: warning: unused variable ‘nsnps’ [-Wunused-variable]
  147 |       int nsnps = toPosition - fromPosition + 1;
      |           ^~~~~
blox.cpp:156:11: warning: unused variable ‘numStrong’ [-Wunused-variable]
  156 |       int numStrong = 0;
      |           ^~~~~~~~~
blox.cpp:157:11: warning: unused variable ‘numRec’ [-Wunused-variable]
  157 |       int numRec = 0;
      |           ^~~~~~
blox.cpp:158:11: warning: unused variable ‘numInGroup’ [-Wunused-variable]
  158 |       int numInGroup = 0;
      |           ^~~~~~~~~~
blox.cpp:226:11: warning: unused variable ‘cnt’ [-Wunused-variable]
  226 |       int cnt = 0;
      |           ^~~
blox.cpp:418:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  418 |       for (int k=0; k<b.size(); k++)
      |                     ~^~~~~~~~~
blox.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  427 |       for (int k=0; k<b.size(); k++)
      |                     ~^~~~~~~~~
blox.cpp:123:16: warning: unused variable ‘fourGameteCutoff’ [-Wunused-variable]
  123 |   const double fourGameteCutoff = 0.01;
      |                ^~~~~~~~~~~~~~~~
blox.cpp: In member function ‘void PairwiseLinkage::calculateCI()’:
blox.cpp:469:7: warning: unused variable ‘total_chroms’ [-Wunused-variable]
  469 |   int total_chroms = knownAA + knownAB + knownBA + knownBB + 2*unknownDH;
      |       ^~~~~~~~~~~~
blox.cpp:569:41: warning: ‘pB2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  569 |   if ( pB1>0 ) loglike1 += knownBA * log( pB1 );
      |                                      ~~~^~~~~~~
blox.cpp:505:10: warning: ‘pB1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  505 |   double p1 = pA1 + pB1;
      |          ^~
blox.cpp:503:10: warning: ‘pA2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  503 |   double pA = pA1 + pA2;
      |          ^~
blox.cpp:510:10: warning: ‘pA1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  510 |   double D = pA1 - (pA*p1);
      |          ^
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zed.cpp
In file included from helper.h:24,
                 from zed.cpp:19:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |               for ( int k = 0 ; k < i->second.size(); k++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c dosage.cpp
In file included from dosage.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |       ^~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c annot.cpp
In file included from annot.cpp:20:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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;
      |                ^~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c metaanal.cpp
In file included from metaanal.cpp:21:
options.h: In member function ‘void OptionSet::display()’:
options.h:73:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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++)
      |                           ~^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c r.cpp
In file included from 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++)
      |                                 ~~^~~~~~~~~~~~~~~~~~
In file included from r.cpp:29:
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’:
Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  203 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’:
Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  206 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’:
Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  232 |     char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; }
      |                                          ~^~~~~
Rconnection.h: In member function ‘void Rstrings::decode()’:
Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare]
  245 |       while (i < len) { if (!c[i]) nel++; i++; }
      |              ~~^~~~~
Rconnection.h:249:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |         while (i < nel) {
      |                ~~^~~~~
r.cpp: In member function ‘void Plink::Rfunc()’:
r.cpp:330:15: warning: unused variable ‘ct’ [-Wunused-variable]
  330 |           int ct = data->length();
      |               ^~
r.cpp:380:16: warning: ‘rCov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  380 |         delete rCov;
      |                ^~~~
r.cpp:378:14: warning: ‘rS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  378 |       delete rS;
      |              ^~
r.cpp:377:14: warning: ‘rP’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  377 |       delete rP;
      |              ^~
r.cpp:376:14: warning: ‘rN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  376 |       delete rN;
      |              ^~
r.cpp:399:10: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  399 |   delete rc;
      |          ^~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c Rconnection.cpp
In file included from Rconnection.h:42,
                 from Rconnection.cpp:30:
Rsrv.h:327:6: warning: #warning using little endian based on information from endian.h [-Wcpp]
  327 |     #warning using little endian based on information from endian.h
      |      ^~~~~~~
In file included from Rconnection.cpp:30:
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(Rmessage*)’:
Rconnection.h:203:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  203 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In constructor ‘Rsymbol::Rsymbol(unsigned int*, Rmessage*)’:
Rconnection.h:206:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  206 |     { name=""; fix_content(); }
      |            ^~
Rconnection.h: In member function ‘char* Rstrings::stringAt(int)’:
Rconnection.h:232:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  232 |     char *stringAt(int i) { return (i<0||i>=nel)?0:cont[i]; }
      |                                          ~^~~~~
Rconnection.h: In member function ‘void Rstrings::decode()’:
Rconnection.h:245:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Rsize_t’ {aka ‘unsigned int’} [-Wsign-compare]
  245 |       while (i < len) { if (!c[i]) nel++; i++; }
      |              ~~^~~~~
Rconnection.h:249:18: 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;
      |                           ^~~~
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -c zfstream.cpp
aarch64-linux-gnu-g++ -Wall -g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DWITH_R_PLUGINS -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DUNIX -O3 -o plink plink.o options.o input.o binput.o tinput.o genome.o helper.o stats.o filters.o locus.o multi.o crandom.o cluster.o mds.o output.o informative.o assoc.o epi.o prephap.o phase.o trio.o tdt.o sharing.o genepi.o sets.o perm.o mh.o genedrop.o gxe.o merge.o hotel.o multiple.o haploCC.o haploTDT.o poo.o webcheck.o qfam.o linear.o bmerge.o parse.o mishap.o legacy.o homozyg.o segment.o model.o logistic.o glm.o dcdflib.o elf.o dfam.o fisher.o linput.o sockets.o lookup.o proxy.o pdriver.o haploQTL.o haplohelper.o haplowindow.o genogroup.o nonfounderphasing.o clumpld.o genoerr.o em.o impute.o metaem.o profile.o nlist.o whap.o simul.o gvar.o cnv.o step.o greport.o flip.o qualscores.o cnvqt.o cfamily.o setscreen.o idhelp.o tag.o hapglm.o lookup2.o blox.o zed.o dosage.o annot.o metaanal.o r.o Rconnection.o zfstream.o -ldl -lcrypt -lz 
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck"
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   dh_installdirs -a
   dh_auto_install --destdir=debian/plink/ -a
   dh_install -a
   dh_installdocs -a
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs debian/upstream.changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
chmod 644 debian/plink/usr/share/doc/plink/examples/*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installman -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'plink' in '../plink_1.07+dfsg-4_arm64.deb'.
dpkg-deb: building package 'plink-dbgsym' in '../plink-dbgsym_1.07+dfsg-4_arm64.deb'.
 dpkg-genbuildinfo --build=any -O../plink_1.07+dfsg-4_arm64.buildinfo
 dpkg-genchanges --build=any -O../plink_1.07+dfsg-4_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-04-02T04:18:06Z

Finished
--------

I: Built successfully

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


plink_1.07+dfsg-4_arm64.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: arm64
Version: 1.07+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
 plink      - whole-genome association analysis toolset
Closes: 984293
Changes:
 plink (1.07+dfsg-4) unstable; urgency=medium
 .
   * Team upload.
   * Add patch to fix FTBFS with gcc-11 (Closes: #984293)
   * Bump Standards-Version to 4.6.0 (no changes needed)
   * Bump debhelper compatibility level to 13
   * Replace ADTTMP with AUTOPKGTEST_TMP
   * Add "Rules-Requires-Root: no"
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+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: plink
Binary: plink plink-dbgsym
Architecture: arm64
Version: 1.07+dfsg-4
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Sat, 02 Apr 2022 04:18:05 +0000
Build-Path: /<<PKGBUILDDIR>>
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 dpkg (= 1.21.7),
 dpkg-dev (= 1.21.7),
 dwz (= 0.14-1),
 file (= 1:5.41-3),
 findutils (= 4.9.0-2),
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 groff-base (= 1.22.4-8),
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 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_US.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1635694306"


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


plink-dbgsym_1.07+dfsg-4_arm64.deb
----------------------------------

 new Debian package, version 2.0.
 size 25789128 bytes: control archive=536 bytes.
     372 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: arm64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 25605
 Depends: plink (= 1.07+dfsg-4)
 Section: debug
 Priority: optional
 Description: debug symbols for plink
 Build-Ids: 93f0d32c49b21834fd2bec379bd56aad55ecd319

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/93/
-rw-r--r-- root/root  26208952 2021-10-31 15:31 ./usr/lib/debug/.build-id/93/f0d32c49b21834fd2bec379bd56aad55ecd319.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_arm64.deb
---------------------------

 new Debian package, version 2.0.
 size 1033404 bytes: control archive=1296 bytes.
    1094 bytes,    26 lines      control              
     915 bytes,    13 lines      md5sums              
 Package: plink
 Version: 1.07+dfsg-4
 Architecture: arm64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3161
 Depends: libc6 (>= 2.29), libcrypt1 (>= 1:4.1.0), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4)
 Recommends: med-config (>= 2.1)
 Section: science
 Priority: optional
 Homepage: http://zzz.bwh.harvard.edu/plink/
 Description: whole-genome association analysis toolset
  plink expects as input the data from SNP (single
  nucleotide polymorphism) chips of many individuals
  and their phenotypical description of a disease.
  It finds associations of single or pairs of DNA
  variations with a phenotype and can retrieve
  SNP annotation from an online source.
  .
  SNPs can evaluated individually or as pairs for their
  association with the disease phenotypes. The joint
  investigation of copy number variations is supported.
  A variety of statistical tests have been implemented.
  .
  Please note: The executable was renamed to plink1
  because of a name clash.  Please read more about this
  in /usr/share/doc/plink/README.Debian.

drwxr-xr-x root/root         0 2021-10-31 15:31 ./
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/bin/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/bin/p-link -> ../lib/debian-med/bin/plink
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/bin/plink1 -> ../lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/bin/
-rwxr-xr-x root/root   3186744 2021-10-31 15:31 ./usr/lib/debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/debian-med/share/man/man1/plink.1.gz -> ../../../../../share/man/man1/p-link.1.gz
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/lib/plink/
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/lib/plink/plink -> ../debian-med/bin/plink
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/
-rw-r--r-- root/root       566 2021-10-31 15:11 ./usr/share/doc/plink/NEWS.Debian.gz
-rw-r--r-- root/root      1894 2021-10-31 15:11 ./usr/share/doc/plink/README.Debian
-rw-r--r-- root/root      1287 2007-07-27 14:51 ./usr/share/doc/plink/README.txt
-rw-r--r-- root/root      2505 2021-10-31 15:31 ./usr/share/doc/plink/changelog.Debian.gz
-rw-r--r-- root/root      8639 2021-10-31 15:11 ./usr/share/doc/plink/changelog.gz
-rw-r--r-- root/root      2290 2021-10-31 15:11 ./usr/share/doc/plink/copyright
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/doc/plink/examples/
-rw-r--r-- root/root       358 2021-10-31 15:11 ./usr/share/doc/plink/examples/README
-rw-r--r-- root/root       267 2021-10-31 15:11 ./usr/share/doc/plink/examples/expected.plink.assoc
-rw-r--r-- root/root       126 2021-10-31 15:11 ./usr/share/doc/plink/examples/expected.plink.frq
-rw-r--r-- root/root        23 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.map
-rw-r--r-- root/root       138 2007-07-27 14:51 ./usr/share/doc/plink/examples/test.ped
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/man/
drwxr-xr-x root/root         0 2021-10-31 15:31 ./usr/share/man/man1/
-rw-r--r-- root/root       688 2021-10-31 15:31 ./usr/share/man/man1/p-link.1.gz
lrwxrwxrwx root/root         0 2021-10-31 15:31 ./usr/share/man/man1/plink1.1.gz -> p-link.1.gz


lintian
-------


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

Merged Build-Depends: lintian: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 [541 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [626 B]
Fetched 2130 B in 0s (81.8 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl
  libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl
  liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl
  libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
  librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
  libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl
  libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip
Suggested packages:
  libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl
  libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libwww-perl
  binutils-multiarch libtext-template-perl zip
Recommended packages:
  gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl
  libpackage-stash-xs-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl
  libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl
  liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl
  libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl
  librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl
  libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
  libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl
  libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzip lzop patchutils
  sbuild-build-depends-lintian-dummy:arm64 t1utils unzip
0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded.
Need to get 7586 kB of archives.
After this operation, 22.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.64-1 [36.6 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.5-1 [51.8 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.27-3+b1 [548 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.38.2-1 [829 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.27-3+b1 [928 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libaliased-perl all 0.34-1.1 [14.1 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40+b1 [72.1 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b4 [11.3 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b3 [16.0 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b4 [25.8 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.31-1 [24.2 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b4 [45.8 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b8 [37.7 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.45-1+b2 [15.5 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-tiny-perl all 2.28-1 [17.3 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-util-perl amd64 1.102-1+b2 [25.7 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-install-perl all 0.928-1.1 [10.8 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libconst-fast-perl all 0.014-1.1 [8552 B]
Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.27-1+b1 [129 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-xs-perl amd64 0.430-2+b1 [40.5 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-dpath-perl all 0.58-1 [43.5 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-1 [35.7 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-netmask-perl all 2.0001-1 [32.2 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-1+b6 [104 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-ip-perl all 0.30-1 [21.0 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b3 [26.1 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-address-xs-perl amd64 1.04-1+b4 [28.0 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.09-1 [16.4 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-2 [7448 B]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.11-2 [8992 B]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libio-prompt-tiny-perl all 0.003-1 [9150 B]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.005004-3 [60.5 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libmouse-perl amd64 2.5.10-1+b2 [173 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b4 [12.1 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1+b2 [13.9 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.122-1 [56.0 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b8 [17.5 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.009-1+b1 [12.2 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.634-1+b1 [46.9 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.023+ds-1 [99.7 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.023+ds-1 [104 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libsort-versions-perl all 1.62-1 [11.0 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.22-1 [51.2 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.27-1 [28.5 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-1+b3 [27.8 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b9 [8800 B]
Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.13-1+b1 [13.6 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-1+b1 [197 kB]
Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b4 [75.8 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b3 [20.3 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 5.10-1 [91.0 kB]
Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.83+ds-1+b1 [35.9 kB]
Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.23-2 [90.0 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-26 [171 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.114.0 [1382 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 7586 kB in 0s (41.0 MB/s)
Selecting previously unselected package diffstat.
(Reading database ... 21434 files and directories currently installed.)
Preparing to unpack .../000-diffstat_1.64-1_amd64.deb ...
Unpacking diffstat (1.64-1) ...
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Preparing to unpack .../001-libassuan0_2.5.5-1_amd64.deb ...
Unpacking libassuan0:amd64 (2.5.5-1) ...
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Preparing to unpack .../013-libmodule-implementation-perl_0.09-1.1_all.deb ...
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Selecting previously unselected package libb-hooks-endofscope-perl.
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Preparing to unpack .../020-libclass-xsaccessor-perl_1.19-3+b8_amd64.deb ...
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Preparing to unpack .../021-libclone-perl_0.45-1+b2_amd64.deb ...
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Preparing to unpack .../024-libsub-install-perl_0.928-1.1_all.deb ...
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Setting up libcpanel-json-xs-perl:amd64 (4.27-1+b1) ...
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Setting up libtime-moment-perl (0.44-1+b4) ...
Setting up libassuan0:amd64 (2.5.5-1) ...
Setting up libconfig-tiny-perl (2.28-1) ...
Setting up libsereal-encoder-perl:amd64 (4.023+ds-1) ...
Setting up liblist-utilsby-perl (0.11-1) ...
Setting up libnet-netmask-perl (2.0001-1) ...
Setting up libsub-install-perl (0.928-1.1) ...
Setting up libnumber-compare-perl (0.03-2) ...
Setting up patchutils (0.4.2-1) ...
Setting up libjson-maybexs-perl (1.004003-1) ...
Setting up libnetaddr-ip-perl (4.079+dfsg-1+b6) ...
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libxs-parse-keyword-perl (0.22-1) ...
Setting up libfile-find-rule-perl (0.34-1) ...
Setting up libipc-system-simple-perl (1.30-1) ...
Setting up libnet-domain-tld-perl (1.75-1.1) ...
Setting up libperlio-utf8-strict-perl (0.009-1+b1) ...
Setting up libio-prompt-tiny-perl (0.003-1) ...
Setting up lzip (1.23-2) ...
update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip (lzip) in auto mode
update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode
update-alternatives: using /usr/bin/lzip.lzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode
Setting up t1utils (1.41-4) ...
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Setting up libb-hooks-op-check-perl (0.22-1+b4) ...
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Setting up libtime-duration-perl (1.21-1) ...
Setting up libtext-xslate-perl:amd64 (3.5.9-1+b1) ...
Setting up libsub-exporter-progressive-perl (0.001013-1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libsub-name-perl (0.26-1+b2) ...
Setting up libsyntax-keyword-try-perl (0.27-1) ...
Setting up libdata-validate-domain-perl (0.10-1.1) ...
Setting up libproc-processtable-perl:amd64 (0.634-1+b1) ...
Setting up libpath-tiny-perl (0.122-1) ...
Setting up lzop (1.04-2) ...
Setting up gpgconf (2.2.27-3+b1) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libipc-run3-perl (0.048-2) ...
Setting up libaliased-perl (0.34-1.1) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006006-1) ...
Setting up libdevel-stacktrace-perl (2.0400-1) ...
Setting up libclass-xsaccessor-perl (1.19-3+b8) ...
Setting up libsort-versions-perl (1.62-1) ...
Setting up libexporter-tiny-perl (1.002002-1) ...
Setting up libterm-readkey-perl (2.38-1+b3) ...
Setting up libfont-ttf-perl (1.06-1.1) ...
Setting up libtext-levenshteinxs-perl (0.03-4+b9) ...
Setting up libperlio-gzip-perl (0.19-1+b8) ...
Setting up libhtml-html5-entities-perl (0.004-1.1) ...
Setting up libsereal-decoder-perl (4.023+ds-1) ...
Setting up libmarkdown2:amd64 (2.2.7-2) ...
Setting up liburi-perl (5.10-1) ...
Setting up libnet-ipv6addr-perl (1.02-1) ...
Setting up gpg (2.2.27-3+b1) ...
Setting up libdata-validate-ip-perl (0.30-1) ...
Setting up libemail-address-xs-perl (1.04-1+b4) ...
Setting up libfile-basedir-perl (0.09-1) ...
Setting up liblist-moreutils-perl (0.430-2) ...
Setting up libtext-markdown-discount-perl:amd64 (0.13-1+b1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl (0.008-1+b3) ...
Setting up libdata-validate-uri-perl (0.07-2) ...
Setting up libdata-optlist-perl (0.112-1) ...
Setting up libsub-exporter-perl (0.988-1) ...
Setting up libiterator-perl (0.03+ds1-1.1) ...
Setting up libiterator-util-perl (0.02+ds1-1.1) ...
Setting up libparams-classify-perl (0.015-1+b4) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libconst-fast-perl (0.014-1.1) ...
Setting up libdata-dpath-perl (0.58-1) ...
Setting up libmodule-implementation-perl (0.09-1.1) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libimport-into-perl (1.002005-1) ...
Setting up libmoo-perl (2.005004-3) ...
Setting up liblist-someutils-perl (0.58-1) ...
Setting up libmoox-aliases-perl (0.001006-1.1) ...
Setting up libb-hooks-endofscope-perl (0.26-1) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.114.0) ...
Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ...
Processing triggers for man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.33-7) ...

I: Lintian run was successful.

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

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| Summary                                                                      |
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Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 393548
Build-Time: 563
Distribution: unstable
Foreign Architectures: arm64
Host Architecture: arm64
Install-Time: 23
Job: plink_1.07+dfsg-4
Lintian: pass
Machine Architecture: amd64
Package: plink
Package-Time: 600
Source-Version: 1.07+dfsg-4
Space: 393548
Status: successful
Version: 1.07+dfsg-4
--------------------------------------------------------------------------------
Finished at 2022-04-02T04:18:06Z
Build needed 00:10:00, 393548k disk space